HEADER TRANSLATION 19-DEC-03 1RY1 TITLE STRUCTURE OF THE SIGNAL RECOGNITION PARTICLE INTERACTING WITH THE TITLE 2 ELONGATION-ARRESTED RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: SRP ALU DOMAIN; COMPND 3 CHAIN: E; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: SRP S DOMAIN; COMPND 6 CHAIN: A; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: SRP RNA; COMPND 9 CHAIN: M; COMPND 10 MOL_ID: 4; COMPND 11 MOLECULE: SRP RNA; COMPND 12 CHAIN: N; COMPND 13 MOL_ID: 5; COMPND 14 MOLECULE: SRP RNA; COMPND 15 CHAIN: O; COMPND 16 MOL_ID: 6; COMPND 17 MOLECULE: SRP RNA; COMPND 18 CHAIN: P; COMPND 19 MOL_ID: 7; COMPND 20 MOLECULE: SRP RNA; COMPND 21 CHAIN: Q; COMPND 22 MOL_ID: 8; COMPND 23 MOLECULE: SRP RNA; COMPND 24 CHAIN: R; COMPND 25 MOL_ID: 9; COMPND 26 MOLECULE: SRP9; COMPND 27 CHAIN: C; COMPND 28 MOL_ID: 10; COMPND 29 MOLECULE: SRP14; COMPND 30 CHAIN: D; COMPND 31 MOL_ID: 11; COMPND 32 MOLECULE: SRP19; COMPND 33 CHAIN: B; COMPND 34 MOL_ID: 12; COMPND 35 MOLECULE: SRP54NG; COMPND 36 CHAIN: U; COMPND 37 MOL_ID: 13; COMPND 38 MOLECULE: SRP54M; COMPND 39 CHAIN: W; COMPND 40 MOL_ID: 14; COMPND 41 MOLECULE: SIGNAL SEQUENCE PEPTIDE; COMPND 42 CHAIN: S; COMPND 43 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 3 ORGANISM_COMMON: DOG; SOURCE 4 ORGANISM_TAXID: 9615; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 7 ORGANISM_COMMON: DOG; SOURCE 8 ORGANISM_TAXID: 9615; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 11 ORGANISM_COMMON: DOG; SOURCE 12 ORGANISM_TAXID: 9615; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 15 ORGANISM_COMMON: DOG; SOURCE 16 ORGANISM_TAXID: 9615; SOURCE 17 MOL_ID: 5; SOURCE 18 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 19 ORGANISM_COMMON: DOG; SOURCE 20 ORGANISM_TAXID: 9615; SOURCE 21 MOL_ID: 6; SOURCE 22 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 23 ORGANISM_COMMON: DOG; SOURCE 24 ORGANISM_TAXID: 9615; SOURCE 25 MOL_ID: 7; SOURCE 26 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 27 ORGANISM_COMMON: DOG; SOURCE 28 ORGANISM_TAXID: 9615; SOURCE 29 MOL_ID: 8; SOURCE 30 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 31 ORGANISM_COMMON: DOG; SOURCE 32 ORGANISM_TAXID: 9615; SOURCE 33 MOL_ID: 9; SOURCE 34 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 35 ORGANISM_COMMON: DOG; SOURCE 36 ORGANISM_TAXID: 9615; SOURCE 37 MOL_ID: 10; SOURCE 38 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 39 ORGANISM_COMMON: DOG; SOURCE 40 ORGANISM_TAXID: 9615; SOURCE 41 MOL_ID: 11; SOURCE 42 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 43 ORGANISM_COMMON: DOG; SOURCE 44 ORGANISM_TAXID: 9615; SOURCE 45 MOL_ID: 12; SOURCE 46 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 47 ORGANISM_COMMON: DOG; SOURCE 48 ORGANISM_TAXID: 9615; SOURCE 49 MOL_ID: 13; SOURCE 50 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 51 ORGANISM_COMMON: DOG; SOURCE 52 ORGANISM_TAXID: 9615; SOURCE 53 MOL_ID: 14; SOURCE 54 SYNTHETIC: YES; SOURCE 55 ORGANISM_SCIENTIFIC: TRITICUM AESTIVUM; SOURCE 56 ORGANISM_COMMON: WHEAT; SOURCE 57 ORGANISM_TAXID: 4565 KEYWDS SIGNAL RECOGNITION PARTICLE, RNA BINDING, TRANSLATION EXPDTA ELECTRON MICROSCOPY AUTHOR M.HALIC,T.BECKER,M.R.POOL,C.M.SPAHN,R.A.GRASSUCCI,J.FRANK,R.BECKMANN REVDAT 5 14-FEB-24 1RY1 1 LINK REVDAT 4 18-JUL-18 1RY1 1 REMARK REVDAT 3 18-APR-18 1RY1 1 COMPND SOURCE DBREF SEQADV REVDAT 2 24-FEB-09 1RY1 1 VERSN REVDAT 1 20-APR-04 1RY1 0 JRNL AUTH M.HALIC,T.BECKER,M.R.POOL,C.M.SPAHN,R.A.GRASSUCCI,J.FRANK, JRNL AUTH 2 R.BECKMANN JRNL TITL STRUCTURE OF THE SIGNAL RECOGNITION PARTICLE INTERACTING JRNL TITL 2 WITH THE ELONGATION-ARRESTED RIBOSOME JRNL REF NATURE V. 427 808 2004 JRNL REFN ISSN 0028-0836 JRNL PMID 14985753 JRNL DOI 10.1038/NATURE02342 REMARK 2 REMARK 2 RESOLUTION. 12.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.00 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THE CHAINS M, N, O, P, Q AND R ARE FRAGMENTS OF A REMARK 3 DOUBLE HELICAL STRAND OF RNA. THE AUTHOR MAINTAINS THAT SOME OF REMARK 3 THE RESIDUES COULD NOT BE MODELED CORRECTLY DUE TO LIMITED REMARK 3 RESOLUTION IN THIS REGION. REMARK 4 REMARK 4 1RY1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021134. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SIGNAL RECOGNITION PARTICLE REMARK 245 INTERACTING WITH ELONGATION- REMARK 245 ARRESTED RIBOSOME; SIGNAL REMARK 245 RECOGNITION PARTICLE; 80S REMARK 245 RIBOSOME NASCENT CHAIN COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO ETHANE REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-JAN-00 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 95.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 10000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 45000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 51000 REMARK 245 CALIBRATED MAGNIFICATION : 52000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 160 REMARK 245 IMAGING DETAILS : SAMPLES WERE MAINTAINED AT REMARK 245 LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE. REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRADECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, A, M, N, O, P, Q, R, C, D, REMARK 350 AND CHAINS: B, U, W, S REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GDP E 99 REMARK 465 C P 251 REMARK 465 PRO C 2 REMARK 465 GLN C 3 REMARK 465 TYR C 4 REMARK 465 LYS C 76 REMARK 465 GLU C 77 REMARK 465 ALA C 78 REMARK 465 ARG C 79 REMARK 465 ASN C 80 REMARK 465 VAL C 81 REMARK 465 THR C 82 REMARK 465 MET C 83 REMARK 465 GLU C 84 REMARK 465 THR C 85 REMARK 465 GLU C 86 REMARK 465 ARG D 36 REMARK 465 THR D 37 REMARK 465 LYS D 38 REMARK 465 PRO D 39 REMARK 465 ILE D 40 REMARK 465 PRO D 41 REMARK 465 LYS D 42 REMARK 465 LYS D 43 REMARK 465 GLY D 44 REMARK 465 THR D 45 REMARK 465 VAL D 46 REMARK 465 GLU D 47 REMARK 465 GLY D 48 REMARK 465 PHE D 49 REMARK 465 GLU D 50 REMARK 465 PRO D 51 REMARK 465 ALA D 52 REMARK 465 ASP D 53 REMARK 465 LYS D 96 REMARK 465 ARG D 97 REMARK 465 ASP D 98 REMARK 465 LYS D 99 REMARK 465 LYS D 100 REMARK 465 ASN D 101 REMARK 465 LYS D 102 REMARK 465 THR D 103 REMARK 465 LYS D 104 REMARK 465 LYS D 105 REMARK 465 THR D 106 REMARK 465 LYS D 107 REMARK 465 MET B 13 REMARK 465 GLY U 295 REMARK 465 ASP U 296 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 U N 301 O3' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N GLY U 289 OD2 ASP W 358 0.27 REMARK 500 C2' G Q 101 OP2 A Q 102 0.39 REMARK 500 C4' A P 252 OP1 A P 253 0.40 REMARK 500 C4' A M 56 CB ASP C 45 0.42 REMARK 500 C ALA U 90 CB MET W 351 0.52 REMARK 500 O2 U N 282 C8 A N 283 0.53 REMARK 500 CD2 TYR U 79 OG1 THR W 357 0.53 REMARK 500 CG ARG W 371 CG2 THR S 62 0.61 REMARK 500 C2' C N 280 O5' A N 281 0.62 REMARK 500 CD GLU U 89 C ILE W 352 0.69 REMARK 500 CZ TYR U 79 CA THR W 357 0.74 REMARK 500 NH1 ARG W 371 O THR S 62 0.77 REMARK 500 N ARG U 91 CG MET W 351 0.78 REMARK 500 OH TYR U 79 C THR W 357 0.79 REMARK 500 O4' A P 252 N6 A Q 102 0.83 REMARK 500 C ARG U 91 SD MET W 351 0.85 REMARK 500 C6 A M 75 O4' G O 76 0.85 REMARK 500 CB ARG U 286 OG SER W 361 0.86 REMARK 500 OE1 GLU U 89 C ILE W 352 0.87 REMARK 500 CD GLU U 89 N PRO W 353 0.89 REMARK 500 C5' C O 92 C5' G O 93 0.89 REMARK 500 NE ARG U 286 O MET W 360 0.90 REMARK 500 N6 A E 126 OP2 C N 293 0.91 REMARK 500 C2 U N 282 N7 A N 283 0.91 REMARK 500 O2' A R 240 C4' C R 242 0.92 REMARK 500 CE2 TYR U 79 CB THR W 357 0.92 REMARK 500 C2 A R 240 O2 C R 242 0.93 REMARK 500 C8 G A 112 C2' C Q 111 0.97 REMARK 500 O2' U N 282 P A N 283 0.99 REMARK 500 CA GLY U 289 CG ASP W 358 0.99 REMARK 500 CG GLU U 89 N PRO W 353 1.00 REMARK 500 O2' U O 97 OP1 G O 98 1.01 REMARK 500 CA ARG U 286 OG SER W 361 1.02 REMARK 500 N9 G A 112 O2' C Q 111 1.02 REMARK 500 O4' A M 56 CB ASP C 45 1.04 REMARK 500 CD ARG W 371 CB THR S 62 1.04 REMARK 500 O2' G Q 101 OP2 A Q 102 1.05 REMARK 500 NZ LYS W 374 O LYS S 67 1.07 REMARK 500 C5' U M 65 OP2 G M 66 1.07 REMARK 500 O2' U N 282 O5' A N 283 1.08 REMARK 500 O2' C N 280 OP2 A N 281 1.08 REMARK 500 C3' A M 56 CA ASP C 45 1.09 REMARK 500 CA GLY U 289 OD1 ASP W 358 1.10 REMARK 500 O4' C E 122 C6 G M 58 1.11 REMARK 500 O2' A R 240 O4' C R 242 1.11 REMARK 500 O5' G E 124 C1' G M 57 1.13 REMARK 500 O ALA U 90 CB MET W 351 1.14 REMARK 500 N1 A M 75 O4' G O 76 1.14 REMARK 500 CG GLU U 89 CD PRO W 353 1.14 REMARK 500 CB ALA U 90 C GLY W 350 1.14 REMARK 500 REMARK 500 THIS ENTRY HAS 393 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 A M 56 O3' G M 57 P 0.100 REMARK 500 G M 74 O3' A M 75 P 0.237 REMARK 500 U N 275 O3' G N 276 P 0.134 REMARK 500 A N 287 O3' G N 288 P -0.080 REMARK 500 U Q 103 O3' C Q 104 P -0.105 REMARK 500 U R 248 O3' G R 249 P 0.203 REMARK 500 PHE W 345 C SER W 346 N -0.423 REMARK 500 LYS W 362 C GLY W 363 N 0.307 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G M 57 O3' - P - O5' ANGL. DEV. = 28.7 DEGREES REMARK 500 G M 57 O3' - P - OP2 ANGL. DEV. = -13.9 DEGREES REMARK 500 G M 57 C3' - O3' - P ANGL. DEV. = -18.5 DEGREES REMARK 500 A M 59 O3' - P - O5' ANGL. DEV. = -20.2 DEGREES REMARK 500 A M 59 O3' - P - OP1 ANGL. DEV. = 9.8 DEGREES REMARK 500 A M 59 C3' - O3' - P ANGL. DEV. = 19.9 DEGREES REMARK 500 U M 65 C3' - O3' - P ANGL. DEV. = -27.4 DEGREES REMARK 500 C M 70 O3' - P - O5' ANGL. DEV. = -68.9 DEGREES REMARK 500 C M 70 O3' - P - OP2 ANGL. DEV. = 7.9 DEGREES REMARK 500 C M 70 O3' - P - OP1 ANGL. DEV. = 12.7 DEGREES REMARK 500 G M 74 C3' - O3' - P ANGL. DEV. = -9.6 DEGREES REMARK 500 A M 75 O3' - P - OP1 ANGL. DEV. = 9.3 DEGREES REMARK 500 U N 275 O3' - P - O5' ANGL. DEV. = -22.8 DEGREES REMARK 500 U N 275 O3' - P - OP1 ANGL. DEV. = 10.7 DEGREES REMARK 500 U N 275 C3' - O3' - P ANGL. DEV. = 35.5 DEGREES REMARK 500 C N 277 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 A N 278 O3' - P - O5' ANGL. DEV. = 50.7 DEGREES REMARK 500 A N 278 O3' - P - OP2 ANGL. DEV. = -24.3 DEGREES REMARK 500 A N 278 O3' - P - OP1 ANGL. DEV. = -21.3 DEGREES REMARK 500 A N 279 O3' - P - O5' ANGL. DEV. = -24.6 DEGREES REMARK 500 A N 279 O3' - P - OP1 ANGL. DEV. = 11.1 DEGREES REMARK 500 C N 280 C3' - O3' - P ANGL. DEV. = -68.7 DEGREES REMARK 500 G N 288 O3' - P - O5' ANGL. DEV. = 18.4 DEGREES REMARK 500 C N 290 O3' - P - O5' ANGL. DEV. = 44.1 DEGREES REMARK 500 C N 290 O3' - P - OP2 ANGL. DEV. = -21.1 DEGREES REMARK 500 C N 290 O3' - P - OP1 ANGL. DEV. = -17.4 DEGREES REMARK 500 C O 84 O3' - P - O5' ANGL. DEV. = 51.6 DEGREES REMARK 500 C O 84 O3' - P - OP2 ANGL. DEV. = -24.7 DEGREES REMARK 500 C O 84 O3' - P - OP1 ANGL. DEV. = -21.7 DEGREES REMARK 500 C O 84 C3' - O3' - P ANGL. DEV. = -21.7 DEGREES REMARK 500 C O 92 O3' - P - O5' ANGL. DEV. = 17.7 DEGREES REMARK 500 C O 92 C3' - O3' - P ANGL. DEV. = -78.4 DEGREES REMARK 500 A P 252 C3' - O3' - P ANGL. DEV. = -54.4 DEGREES REMARK 500 C P 265 O3' - P - O5' ANGL. DEV. = -38.5 DEGREES REMARK 500 C P 265 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 C P 265 O3' - P - OP1 ANGL. DEV. = 14.1 DEGREES REMARK 500 C P 265 C3' - O3' - P ANGL. DEV. = -28.0 DEGREES REMARK 500 G Q 101 O3' - P - O5' ANGL. DEV. = 54.0 DEGREES REMARK 500 G Q 101 O3' - P - OP2 ANGL. DEV. = -25.8 DEGREES REMARK 500 G Q 101 O3' - P - OP1 ANGL. DEV. = -23.1 DEGREES REMARK 500 G Q 101 C3' - O3' - P ANGL. DEV. = -48.3 DEGREES REMARK 500 C Q 104 O3' - P - O5' ANGL. DEV. = -53.2 DEGREES REMARK 500 C Q 104 O3' - P - OP2 ANGL. DEV. = 8.4 DEGREES REMARK 500 C Q 104 O3' - P - OP1 ANGL. DEV. = 14.9 DEGREES REMARK 500 U R 241 O3' - P - O5' ANGL. DEV. = -29.0 DEGREES REMARK 500 U R 241 O3' - P - OP1 ANGL. DEV. = 12.3 DEGREES REMARK 500 G R 243 C3' - O3' - P ANGL. DEV. = 21.8 DEGREES REMARK 500 U R 248 C3' - O3' - P ANGL. DEV. = 17.2 DEGREES REMARK 500 G R 249 O3' - P - O5' ANGL. DEV. = -49.7 DEGREES REMARK 500 G R 249 O3' - P - OP1 ANGL. DEV. = 39.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 60 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP C 21 89.08 -168.40 REMARK 500 PRO C 22 7.08 -68.89 REMARK 500 ARG C 32 78.44 -117.75 REMARK 500 SER C 34 -88.24 -49.15 REMARK 500 LEU C 46 15.76 -156.87 REMARK 500 VAL C 47 91.01 -172.04 REMARK 500 SER D 6 -68.37 -5.84 REMARK 500 GLU D 7 -84.98 -56.30 REMARK 500 GLN D 8 -59.84 -14.38 REMARK 500 CYS D 20 4.57 -151.66 REMARK 500 ASP D 34 -87.82 -136.41 REMARK 500 PHE B 15 175.01 -56.36 REMARK 500 ALA B 40 177.23 -57.78 REMARK 500 GLU B 42 -97.61 -43.53 REMARK 500 ALA B 55 44.45 -95.69 REMARK 500 VAL B 56 -8.82 -150.14 REMARK 500 LYS B 64 -45.33 -28.39 REMARK 500 ARG B 70 37.05 -92.81 REMARK 500 ASP B 75 -177.21 -50.48 REMARK 500 LEU B 86 -74.77 -93.07 REMARK 500 GLU B 89 -35.65 -35.65 REMARK 500 VAL B 96 -37.85 -35.66 REMARK 500 PRO B 99 -82.10 -69.06 REMARK 500 PRO B 113 11.76 -64.26 REMARK 500 ARG U 21 137.38 65.56 REMARK 500 GLU U 66 51.91 -104.05 REMARK 500 THR U 69 88.15 -153.48 REMARK 500 LYS U 96 -151.61 -115.45 REMARK 500 VAL U 237 -42.46 -130.44 REMARK 500 ARG U 252 -72.59 -91.11 REMARK 500 SER U 273 163.50 177.58 REMARK 500 PRO W 344 -90.43 -52.82 REMARK 500 PHE W 345 -46.04 25.38 REMARK 500 SER W 346 -29.53 -35.88 REMARK 500 MET W 360 66.96 65.25 REMARK 500 LYS W 362 -95.54 104.95 REMARK 500 ASN W 364 55.46 -110.90 REMARK 500 PRO W 400 -7.88 -56.87 REMARK 500 PHE S 52 -70.55 -68.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO W 344 PHE W 345 146.52 REMARK 500 SER W 361 LYS W 362 -134.81 REMARK 500 LYS W 362 GLY W 363 -145.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A 197 0.07 SIDE CHAIN REMARK 500 A A 201 0.06 SIDE CHAIN REMARK 500 A A 208 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO W 344 21.31 REMARK 500 SER W 361 -13.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1063 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS STRUCTURE HAS BEEN MODELED USING POLYMER SEQUENCES FROM OTHER REMARK 999 ORGANISMS, INCLUDING HOMO SAPIENS (CHAINS C,D,E), THERMUS AQUATICUS REMARK 999 (CHAIN U), MUS MUSCULUS (CHAIN W), AND TURSIOPS TRUNCATUS (CHAIN S). DBREF 1RY1 E 99 148 PDB 1RY1 1RY1 99 148 DBREF 1RY1 A 112 239 PDB 1RY1 1RY1 112 239 DBREF 1RY1 M 49 75 PDB 1RY1 1RY1 49 75 DBREF 1RY1 N 271 301 PDB 1RY1 1RY1 271 301 DBREF 1RY1 O 76 99 PDB 1RY1 1RY1 76 99 DBREF 1RY1 P 251 270 PDB 1RY1 1RY1 251 270 DBREF 1RY1 Q 100 111 PDB 1RY1 1RY1 100 111 DBREF 1RY1 R 240 251 PDB 1RY1 1RY1 240 251 DBREF 1RY1 C 2 86 PDB 1RY1 1RY1 2 86 DBREF 1RY1 D 2 107 UNP P37108 SRP14_HUMAN 2 107 DBREF 1RY1 B 13 120 PDB 1RY1 1RY1 13 120 DBREF 1RY1 U 1 296 PDB 1RY1 1RY1 1 296 DBREF 1RY1 W 326 434 PDB 1RY1 1RY1 326 434 DBREF 1RY1 S 50 67 PDB 1RY1 1RY1 50 67 SEQRES 1 E 50 GDP G G C C G G G C G C G G SEQRES 2 E 50 U G G C G C G C G C C U G SEQRES 3 E 50 U A G U C C C A G C U A C SEQRES 4 E 50 U C G G G A G G C U C SEQRES 1 A 128 G A C A C U A A G U U C G SEQRES 2 A 128 G C A U C A A U A U G G U SEQRES 3 A 128 G A C C U C C C G G G A G SEQRES 4 A 128 C G G G G G A C C A C C A SEQRES 5 A 128 G G U U G C C U A A G G A SEQRES 6 A 128 G G G G U G A A C C G G C SEQRES 7 A 128 C C A G G U C G G A A A C SEQRES 8 A 128 G G A G C A G G U C A A A SEQRES 9 A 128 A C U C C C G U G C U G A SEQRES 10 A 128 U C A G U A G U G U CCC SEQRES 1 M 27 A G G C U G G A G G A U C SEQRES 2 M 27 G C U U G A G U C C A G G SEQRES 3 M 27 A SEQRES 1 N 31 C C U G U G C A A C A U A SEQRES 2 N 31 G C G A G A C C C C G U C SEQRES 3 N 31 U C U U U SEQRES 1 O 24 G U U C U G G G C U G U A SEQRES 2 O 24 G U G C G C U A U G C SEQRES 1 P 20 C A A U A G C C A C U G C SEQRES 2 P 20 A C U C C A G SEQRES 1 Q 12 C G A U C G G G U G U C SEQRES 1 R 12 A U C G C G C C U G U G SEQRES 1 C 85 PRO GLN TYR GLN THR TRP GLU GLU PHE SER ARG ALA ALA SEQRES 2 C 85 GLU LYS LEU TYR LEU ALA ASP PRO MET LYS ALA ARG VAL SEQRES 3 C 85 VAL LEU LYS TYR ARG HIS SER ASP GLY ASN LEU CYS VAL SEQRES 4 C 85 LYS VAL THR ASP ASP LEU VAL CYS LEU VAL TYR LYS THR SEQRES 5 C 85 ASP GLN ALA GLN ASP VAL LYS LYS ILE GLU LYS PHE HIS SEQRES 6 C 85 SER GLN LEU MET ARG LEU MET VAL ALA LYS GLU ALA ARG SEQRES 7 C 85 ASN VAL THR MET GLU THR GLU SEQRES 1 D 106 VAL LEU LEU GLU SER GLU GLN PHE LEU THR GLU LEU THR SEQRES 2 D 106 ARG LEU PHE GLN LYS CYS ARG THR SER GLY SER VAL TYR SEQRES 3 D 106 ILE THR LEU LYS LYS TYR ASP GLY ARG THR LYS PRO ILE SEQRES 4 D 106 PRO LYS LYS GLY THR VAL GLU GLY PHE GLU PRO ALA ASP SEQRES 5 D 106 ASN LYS CYS LEU LEU ARG ALA THR ASP GLY LYS LYS LYS SEQRES 6 D 106 ILE SER THR VAL VAL SER SER LYS GLU VAL ASN LYS PHE SEQRES 7 D 106 GLN MET ALA TYR SER ASN LEU LEU ARG ALA ASN MET ASP SEQRES 8 D 106 GLY LEU LYS LYS ARG ASP LYS LYS ASN LYS THR LYS LYS SEQRES 9 D 106 THR LYS SEQRES 1 B 108 MET ARG PHE ILE CYS ILE TYR PRO ALA TYR LEU ASN ASN SEQRES 2 B 108 LYS LYS THR ILE ALA GLU GLY ARG ARG ILE PRO ILE SER SEQRES 3 B 108 LYS ALA VAL GLU ASN PRO THR ALA THR GLU ILE GLN ASP SEQRES 4 B 108 VAL CYS SER ALA VAL GLY LEU ASN VAL PHE LEU GLU LYS SEQRES 5 B 108 ASN LYS MET TYR SER ARG GLU TRP ASN ARG ASP VAL GLN SEQRES 6 B 108 TYR ARG GLY ARG VAL ARG VAL GLN LEU LYS GLN GLU ASP SEQRES 7 B 108 GLY SER LEU CYS LEU VAL GLN PHE PRO SER ARG LYS SER SEQRES 8 B 108 VAL MET LEU TYR ALA ALA GLU MET ILE PRO LYS LEU LYS SEQRES 9 B 108 THR ARG THR GLN SEQRES 1 U 296 MET PHE GLN GLN LEU SER ALA ARG LEU GLN GLU ALA ILE SEQRES 2 U 296 GLY ARG LEU ARG GLY ARG GLY ARG ILE THR GLU GLU ASP SEQRES 3 U 296 LEU LYS ALA THR LEU ARG GLU ILE ARG ARG ALA LEU MET SEQRES 4 U 296 ASP ALA ASP VAL ASN LEU GLU VAL ALA ARG ASP PHE VAL SEQRES 5 U 296 GLU ARG VAL ARG GLU GLU ALA LEU GLY LYS GLN VAL LEU SEQRES 6 U 296 GLU SER LEU THR PRO ALA GLU VAL ILE LEU ALA THR VAL SEQRES 7 U 296 TYR GLU ALA LEU LYS GLU ALA LEU GLY GLY GLU ALA ARG SEQRES 8 U 296 LEU PRO VAL LEU LYS ASP ARG ASN LEU TRP PHE LEU VAL SEQRES 9 U 296 GLY LEU GLN GLY SER GLY LYS THR THR THR ALA ALA LYS SEQRES 10 U 296 LEU ALA LEU TYR TYR LYS GLY LYS GLY ARG ARG PRO LEU SEQRES 11 U 296 LEU VAL ALA ALA ASP THR GLN ARG PRO ALA ALA ARG GLU SEQRES 12 U 296 GLN LEU ARG LEU LEU GLY GLU LYS VAL GLY VAL PRO VAL SEQRES 13 U 296 LEU GLU VAL MET ASP GLY GLU SER PRO GLU SER ILE ARG SEQRES 14 U 296 ARG ARG VAL GLU GLU LYS ALA ARG LEU GLU ALA ARG ASP SEQRES 15 U 296 LEU ILE LEU VAL ASP THR ALA GLY ARG LEU GLN ILE ASP SEQRES 16 U 296 GLU PRO LEU MET GLY GLU LEU ALA ARG LEU LYS GLU VAL SEQRES 17 U 296 LEU GLY PRO ASP GLU VAL LEU LEU VAL LEU ASP ALA MET SEQRES 18 U 296 THR GLY GLN GLU ALA LEU SER VAL ALA ARG ALA PHE ASP SEQRES 19 U 296 GLU LYS VAL GLY VAL THR GLY LEU VAL LEU THR LYS LEU SEQRES 20 U 296 ASP GLY ASP ALA ARG GLY GLY ALA ALA LEU SER ALA ARG SEQRES 21 U 296 HIS VAL THR GLY LYS PRO ILE TYR PHE ALA GLY VAL SER SEQRES 22 U 296 GLU LYS PRO GLU GLY LEU GLU PRO PHE TYR PRO GLU ARG SEQRES 23 U 296 LEU ALA GLY ARG ILE LEU GLY MET GLY ASP SEQRES 1 W 109 GLN PHE THR LEU ARG ASP MET TYR GLU GLN PHE GLN ASN SEQRES 2 W 109 ILE MET LYS MET GLY PRO PHE SER GLN ILE LEU GLY MET SEQRES 3 W 109 ILE PRO GLY PHE GLY THR ASP PHE MET SER LYS GLY ASN SEQRES 4 W 109 GLU GLN GLU SER MET ALA ARG LEU LYS LYS LEU MET THR SEQRES 5 W 109 ILE MET ASP SER MET ASN ASP GLN GLU LEU ASP SER THR SEQRES 6 W 109 ASP GLY ALA LYS VAL PHE SER LYS GLN PRO GLY ARG ILE SEQRES 7 W 109 GLN ARG VAL ALA ARG GLY SER GLY VAL SER THR ARG ASP SEQRES 8 W 109 VAL GLN GLU LEU LEU THR GLN TYR THR LYS PHE ALA GLN SEQRES 9 W 109 MET VAL LYS LYS MET SEQRES 1 S 18 LEU GLY PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR SEQRES 2 S 18 VAL GLN HIS LYS LYS MODRES 1RY1 CCC A 239 C HET CCC A 239 23 HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE FORMUL 2 CCC C9 H13 N3 O10 P2 HELIX 1 1 GLN C 5 ASP C 21 1 17 HELIX 2 2 GLN C 55 GLN C 57 5 3 HELIX 3 3 ASP C 58 ALA C 75 1 18 HELIX 4 4 GLU D 5 LYS D 19 1 15 HELIX 5 5 GLU D 75 MET D 91 1 17 HELIX 6 6 TYR B 19 ASN B 24 5 6 HELIX 7 7 THR B 45 SER B 54 1 10 HELIX 8 8 ALA B 55 GLY B 57 5 3 HELIX 9 9 ARG B 101 ILE B 112 1 12 HELIX 10 10 LEU B 115 GLN B 120 1 6 HELIX 11 11 PHE U 2 ARG U 15 1 14 HELIX 12 12 LEU U 16 GLY U 20 5 5 HELIX 13 13 THR U 23 ALA U 41 1 19 HELIX 14 14 ASN U 44 LYS U 62 1 19 HELIX 15 15 GLN U 63 SER U 67 5 5 HELIX 16 16 THR U 69 GLY U 87 1 19 HELIX 17 17 GLY U 110 GLY U 124 1 15 HELIX 18 18 ARG U 138 GLY U 153 1 16 HELIX 19 19 SER U 164 ALA U 180 1 17 HELIX 20 20 ASP U 195 GLY U 210 1 16 HELIX 21 21 MET U 221 GLY U 223 5 3 HELIX 22 22 GLN U 224 VAL U 237 1 14 HELIX 23 23 GLY U 253 GLY U 264 1 12 HELIX 24 24 TYR U 283 GLY U 293 1 11 HELIX 25 25 THR W 328 MET W 342 1 15 HELIX 26 26 PHE W 345 GLY W 350 1 6 HELIX 27 27 GLU W 365 ASP W 380 1 16 HELIX 28 28 ASN W 383 SER W 389 1 7 HELIX 29 29 ASP W 391 GLN W 399 1 9 HELIX 30 30 PRO W 400 SER W 410 1 11 HELIX 31 31 SER W 413 LYS W 433 1 21 HELIX 32 32 LEU S 50 HIS S 65 1 16 SHEET 1 A 6 LEU C 49 THR C 53 0 SHEET 2 A 6 LEU C 38 THR C 43 -1 N VAL C 40 O TYR C 51 SHEET 3 A 6 ARG C 26 LEU C 29 -1 N VAL C 28 O LYS C 41 SHEET 4 A 6 TYR D 27 TYR D 33 -1 O LEU D 30 N VAL C 27 SHEET 5 A 6 LYS D 55 THR D 61 -1 O LEU D 57 N LYS D 31 SHEET 6 A 6 LYS D 66 SER D 72 -1 O ILE D 67 N ALA D 60 SHEET 1 B 3 ILE B 16 ILE B 18 0 SHEET 2 B 3 ARG B 81 GLN B 85 -1 O VAL B 84 N ILE B 16 SHEET 3 B 3 ASN B 59 GLU B 63 -1 N GLU B 63 O ARG B 81 SHEET 1 C 8 VAL U 156 GLU U 158 0 SHEET 2 C 8 PRO U 129 ALA U 133 1 N LEU U 131 O LEU U 157 SHEET 3 C 8 LEU U 183 ASP U 187 1 O LEU U 185 N LEU U 130 SHEET 4 C 8 ASN U 99 VAL U 104 1 N TRP U 101 O VAL U 186 SHEET 5 C 8 GLU U 213 ASP U 219 1 O VAL U 217 N VAL U 104 SHEET 6 C 8 GLY U 241 THR U 245 1 O GLY U 241 N LEU U 216 SHEET 7 C 8 ILE U 267 GLY U 271 1 O GLY U 271 N LEU U 244 SHEET 8 C 8 LEU U 279 PRO U 281 -1 O GLU U 280 N ALA U 270 LINK O3' U A 238 P CCC A 239 1555 1555 1.61 LINK O2C CCC A 239 C2' C R 242 1555 1555 1.87 LINK O2C CCC A 239 O2' C R 242 1555 1555 1.11 LINK PC CCC A 239 O2' C R 242 1555 1555 1.29 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000