HEADER RNA BINDING PROTEIN/RNA 16-FEB-05 1YVP TITLE RO AUTOANTIGEN COMPLEXED WITH RNAS CAVEAT 1YVP INCORRECT CHIRALITY OF ONE C1' RIBOSE CARBON COMPND MOL_ID: 1; COMPND 2 MOLECULE: Y RNA SEQUENCE, FIRST STRAND; COMPND 3 CHAIN: C, E, G, H; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CHAINS G AND H ARE SINGLE STRANDS BOUND BY PROTEIN; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: Y RNA SEQUENCE, SECOND STRAND; COMPND 8 CHAIN: D, F; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 60-KDA SS-A/RO RIBONUCLEOPROTEIN; COMPND 12 CHAIN: A, B; COMPND 13 SYNONYM: RO AUTOANTIGEN; 60 KDA RO PROTEIN; 60 KDA RIBONUCLEOPROTEIN COMPND 14 RO; RORNP; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: PROTEIN A BINDS RNA CHAIN G, B BINDS H SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 7 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 8 ORGANISM_TAXID: 8355; SOURCE 9 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 10 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: TN5 B1-4; SOURCE 13 EXPRESSION_SYSTEM_ORGAN: EGGS; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS HEAT REPEAT; VON WILLEBRAND FACTOR A; ROSSMANN FOLD; MIDAS MOTIF; RNA KEYWDS 2 DUPLEX; SSRNA, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.J.STEIN,G.FUCHS,C.FU,S.L.WOLIN,K.M.REINISCH REVDAT 4 14-FEB-24 1YVP 1 REMARK LINK REVDAT 3 28-DEC-11 1YVP 1 CAVEAT VERSN REVDAT 2 24-FEB-09 1YVP 1 VERSN REVDAT 1 07-JUN-05 1YVP 0 JRNL AUTH A.J.STEIN,G.FUCHS,C.FU,S.L.WOLIN,K.M.REINISCH JRNL TITL STRUCTURAL INSIGHTS INTO RNA QUALITY CONTROL: THE RO JRNL TITL 2 AUTOANTIGEN BINDS MISFOLDED RNAS VIA ITS CENTRAL CAVITY JRNL REF CELL(CAMBRIDGE,MASS.) V. 121 529 2005 JRNL REFN ISSN 0092-8674 JRNL PMID 15907467 JRNL DOI 10.1016/J.CELL.2005.03.009 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 70300 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7098 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8378 REMARK 3 NUCLEIC ACID ATOMS : 1094 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.269 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YVP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000031972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 3.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72908 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SOLVE, CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM ACETATE, MAGNESIUM REMARK 280 ACETATE, DTT, PH 3.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 76.82500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, H, B 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 G G 1 REMARK 465 C G 2 REMARK 465 IU G 3 REMARK 465 G G 4 REMARK 465 G G 5 REMARK 465 G H 1 REMARK 465 C H 2 REMARK 465 IU H 3 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 ASN A 337 REMARK 465 ARG A 338 REMARK 465 GLY A 339 REMARK 465 LYS A 340 REMARK 465 ILE A 538 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 ALA B 3 REMARK 465 ARG B 338 REMARK 465 GLY B 339 REMARK 465 ILE B 538 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 G 6 P OP1 OP2 REMARK 470 G H 4 P OP1 OP2 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 U G 6 N1 - C1' - C2' ANGL. DEV. = 10.4 DEGREES REMARK 500 C G 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 G G 9 N9 - C1' - C2' ANGL. DEV. = 8.3 DEGREES REMARK 500 G H 9 N9 - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 523 N - CA - C ANGL. DEV. = -17.1 DEGREES REMARK 500 ASP B 523 N - CA - C ANGL. DEV. = -17.0 DEGREES 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 CYS A 102 -13.50 56.02 REMARK 500 LYS A 140 63.01 36.61 REMARK 500 TRP A 144 46.27 -88.81 REMARK 500 ASN A 175 41.03 37.72 REMARK 500 GLU A 215 14.98 55.79 REMARK 500 LEU A 294 67.48 -115.41 REMARK 500 ALA A 297 6.07 59.98 REMARK 500 SER A 416 -102.93 -131.85 REMARK 500 SER A 438 31.01 -84.50 REMARK 500 CYS A 470 18.71 59.62 REMARK 500 GLU A 471 53.97 -91.26 REMARK 500 ASN A 473 40.28 -152.93 REMARK 500 ARG A 514 -5.84 -57.84 REMARK 500 ASP A 536 16.31 57.75 REMARK 500 ASN B 12 -179.17 -170.20 REMARK 500 CYS B 102 -24.30 73.12 REMARK 500 GLU B 137 -76.99 -41.64 REMARK 500 LYS B 140 29.75 38.63 REMARK 500 TRP B 144 42.46 -93.72 REMARK 500 TYR B 171 75.75 -118.62 REMARK 500 LYS B 214 93.31 -44.63 REMARK 500 GLU B 215 78.24 41.29 REMARK 500 GLU B 217 83.08 -58.84 REMARK 500 SER B 219 159.91 -47.13 REMARK 500 PRO B 220 25.71 -65.76 REMARK 500 GLU B 221 -47.95 -130.12 REMARK 500 LEU B 263 5.26 -63.42 REMARK 500 LEU B 294 69.77 -115.12 REMARK 500 SER B 416 -105.70 -140.08 REMARK 500 MET B 442 151.80 178.61 REMARK 500 ASN B 473 38.12 -161.50 REMARK 500 SER B 524 -9.20 -55.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 378 OG REMARK 620 2 SER A 380 OG 92.3 REMARK 620 3 THR A 445 OG1 85.1 160.0 REMARK 620 4 ACT A2001 OXT 78.0 99.6 99.3 REMARK 620 5 HOH A2167 O 155.0 100.0 75.9 120.6 REMARK 620 6 HOH A2168 O 82.8 79.2 80.7 160.7 78.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 378 OG REMARK 620 2 SER B 380 OG 96.9 REMARK 620 3 THR B 445 OG1 81.8 167.2 REMARK 620 4 ACT B2002 OXT 88.8 89.8 102.9 REMARK 620 5 HOH B2170 O 160.7 94.1 84.0 107.2 REMARK 620 6 HOH B2171 O 88.7 83.9 83.3 172.8 76.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YVR RELATED DB: PDB REMARK 900 RO AUTOANTIGEN, NO RNA DBREF 1YVP A 1 538 UNP P42700 RO60_XENLA 1 538 DBREF 1YVP B 1 538 UNP P42700 RO60_XENLA 1 538 DBREF 1YVP C 1 10 PDB 1YVP 1YVP 1 10 DBREF 1YVP D 1 10 PDB 1YVP 1YVP 1 10 DBREF 1YVP E 1 10 PDB 1YVP 1YVP 1 10 DBREF 1YVP F 1 10 PDB 1YVP 1YVP 1 10 DBREF 1YVP G 1 10 PDB 1YVP 1YVP 1 10 DBREF 1YVP H 1 10 PDB 1YVP 1YVP 1 10 SEQRES 1 C 10 G C IU G G U C C G A SEQRES 1 D 10 IU IU G A C IU A G C C SEQRES 1 E 10 G C IU G G U C C G A SEQRES 1 F 10 IU IU G A C IU A G C C SEQRES 1 G 10 G C IU G G U C C G A SEQRES 1 H 10 G C IU G G U C C G A SEQRES 1 A 538 MET GLU ALA THR MET ASP GLN THR GLN PRO LEU ASN GLU SEQRES 2 A 538 LYS GLN VAL PRO ASN SER GLU GLY CYS TYR VAL TRP GLN SEQRES 3 A 538 VAL SER ASP MET ASN ARG LEU ARG ARG PHE LEU CYS PHE SEQRES 4 A 538 GLY SER GLU GLY GLY THR TYR TYR ILE GLU GLU LYS LYS SEQRES 5 A 538 LEU GLY GLN GLU ASN ALA GLU ALA LEU LEU ARG LEU ILE SEQRES 6 A 538 GLU ASP GLY LYS GLY CYS GLU VAL VAL GLN GLU ILE LYS SEQRES 7 A 538 THR PHE SER GLN GLU GLY ARG ALA ALA LYS GLN GLU PRO SEQRES 8 A 538 THR LEU PHE ALA LEU ALA VAL CYS SER GLN CYS SER ASP SEQRES 9 A 538 ILE LYS THR LYS GLN ALA ALA PHE ARG ALA VAL PRO GLU SEQRES 10 A 538 VAL CYS ARG ILE PRO THR HIS LEU PHE THR PHE ILE GLN SEQRES 11 A 538 PHE LYS LYS ASP LEU LYS GLU GLY MET LYS CYS GLY MET SEQRES 12 A 538 TRP GLY ARG ALA LEU ARG LYS ALA VAL SER ASP TRP TYR SEQRES 13 A 538 ASN THR LYS ASP ALA LEU ASN LEU ALA MET ALA VAL THR SEQRES 14 A 538 LYS TYR LYS GLN ARG ASN GLY TRP SER HIS LYS ASP LEU SEQRES 15 A 538 LEU ARG LEU SER HIS ILE LYS PRO ALA ASN GLU GLY LEU SEQRES 16 A 538 THR MET VAL ALA LYS TYR VAL SER LYS GLY TRP LYS GLU SEQRES 17 A 538 VAL GLN GLU ALA TYR LYS GLU LYS GLU LEU SER PRO GLU SEQRES 18 A 538 THR GLU LYS VAL LEU LYS TYR LEU GLU ALA THR GLU ARG SEQRES 19 A 538 VAL LYS ARG THR LYS ASP GLU LEU GLU ILE ILE HIS LEU SEQRES 20 A 538 ILE ASP GLU TYR ARG LEU VAL ARG GLU HIS LEU LEU THR SEQRES 21 A 538 ILE HIS LEU LYS SER LYS GLU ILE TRP LYS SER LEU LEU SEQRES 22 A 538 GLN ASP MET PRO LEU THR ALA LEU LEU ARG ASN LEU GLY SEQRES 23 A 538 LYS MET THR ALA ASP SER VAL LEU ALA PRO ALA SER SER SEQRES 24 A 538 GLU VAL SER SER VAL CYS GLU ARG LEU THR ASN GLU LYS SEQRES 25 A 538 LEU LEU LYS LYS ALA ARG ILE HIS PRO PHE HIS ILE LEU SEQRES 26 A 538 VAL ALA LEU GLU THR TYR LYS LYS GLY HIS GLY ASN ARG SEQRES 27 A 538 GLY LYS LEU ARG TRP ILE PRO ASP THR SER ILE VAL GLU SEQRES 28 A 538 ALA LEU ASP ASN ALA PHE TYR LYS SER PHE LYS LEU VAL SEQRES 29 A 538 GLU PRO THR GLY LYS ARG PHE LEU LEU ALA ILE ASP VAL SEQRES 30 A 538 SER ALA SER MET ASN GLN ARG VAL LEU GLY SER ILE LEU SEQRES 31 A 538 ASN ALA SER VAL VAL ALA ALA ALA MET CYS MET LEU VAL SEQRES 32 A 538 ALA ARG THR GLU LYS ASP SER HIS MET VAL ALA PHE SER SEQRES 33 A 538 ASP GLU MET LEU PRO CYS PRO ILE THR VAL ASN MET LEU SEQRES 34 A 538 LEU HIS GLU VAL VAL GLU LYS MET SER ASP ILE THR MET SEQRES 35 A 538 GLY SER THR ASP CYS ALA LEU PRO MET LEU TRP ALA GLN SEQRES 36 A 538 LYS THR ASN THR ALA ALA ASP ILE PHE ILE VAL PHE THR SEQRES 37 A 538 ASP CYS GLU THR ASN VAL GLU ASP VAL HIS PRO ALA THR SEQRES 38 A 538 ALA LEU LYS GLN TYR ARG GLU LYS MET GLY ILE PRO ALA SEQRES 39 A 538 LYS LEU ILE VAL CYS ALA MET THR SER ASN GLY PHE SER SEQRES 40 A 538 ILE ALA ASP PRO ASP ASP ARG GLY MET LEU ASP ILE CYS SEQRES 41 A 538 GLY PHE ASP SER GLY ALA LEU ASP VAL ILE ARG ASN PHE SEQRES 42 A 538 THR LEU ASP LEU ILE SEQRES 1 B 538 MET GLU ALA THR MET ASP GLN THR GLN PRO LEU ASN GLU SEQRES 2 B 538 LYS GLN VAL PRO ASN SER GLU GLY CYS TYR VAL TRP GLN SEQRES 3 B 538 VAL SER ASP MET ASN ARG LEU ARG ARG PHE LEU CYS PHE SEQRES 4 B 538 GLY SER GLU GLY GLY THR TYR TYR ILE GLU GLU LYS LYS SEQRES 5 B 538 LEU GLY GLN GLU ASN ALA GLU ALA LEU LEU ARG LEU ILE SEQRES 6 B 538 GLU ASP GLY LYS GLY CYS GLU VAL VAL GLN GLU ILE LYS SEQRES 7 B 538 THR PHE SER GLN GLU GLY ARG ALA ALA LYS GLN GLU PRO SEQRES 8 B 538 THR LEU PHE ALA LEU ALA VAL CYS SER GLN CYS SER ASP SEQRES 9 B 538 ILE LYS THR LYS GLN ALA ALA PHE ARG ALA VAL PRO GLU SEQRES 10 B 538 VAL CYS ARG ILE PRO THR HIS LEU PHE THR PHE ILE GLN SEQRES 11 B 538 PHE LYS LYS ASP LEU LYS GLU GLY MET LYS CYS GLY MET SEQRES 12 B 538 TRP GLY ARG ALA LEU ARG LYS ALA VAL SER ASP TRP TYR SEQRES 13 B 538 ASN THR LYS ASP ALA LEU ASN LEU ALA MET ALA VAL THR SEQRES 14 B 538 LYS TYR LYS GLN ARG ASN GLY TRP SER HIS LYS ASP LEU SEQRES 15 B 538 LEU ARG LEU SER HIS ILE LYS PRO ALA ASN GLU GLY LEU SEQRES 16 B 538 THR MET VAL ALA LYS TYR VAL SER LYS GLY TRP LYS GLU SEQRES 17 B 538 VAL GLN GLU ALA TYR LYS GLU LYS GLU LEU SER PRO GLU SEQRES 18 B 538 THR GLU LYS VAL LEU LYS TYR LEU GLU ALA THR GLU ARG SEQRES 19 B 538 VAL LYS ARG THR LYS ASP GLU LEU GLU ILE ILE HIS LEU SEQRES 20 B 538 ILE ASP GLU TYR ARG LEU VAL ARG GLU HIS LEU LEU THR SEQRES 21 B 538 ILE HIS LEU LYS SER LYS GLU ILE TRP LYS SER LEU LEU SEQRES 22 B 538 GLN ASP MET PRO LEU THR ALA LEU LEU ARG ASN LEU GLY SEQRES 23 B 538 LYS MET THR ALA ASP SER VAL LEU ALA PRO ALA SER SER SEQRES 24 B 538 GLU VAL SER SER VAL CYS GLU ARG LEU THR ASN GLU LYS SEQRES 25 B 538 LEU LEU LYS LYS ALA ARG ILE HIS PRO PHE HIS ILE LEU SEQRES 26 B 538 VAL ALA LEU GLU THR TYR LYS LYS GLY HIS GLY ASN ARG SEQRES 27 B 538 GLY LYS LEU ARG TRP ILE PRO ASP THR SER ILE VAL GLU SEQRES 28 B 538 ALA LEU ASP ASN ALA PHE TYR LYS SER PHE LYS LEU VAL SEQRES 29 B 538 GLU PRO THR GLY LYS ARG PHE LEU LEU ALA ILE ASP VAL SEQRES 30 B 538 SER ALA SER MET ASN GLN ARG VAL LEU GLY SER ILE LEU SEQRES 31 B 538 ASN ALA SER VAL VAL ALA ALA ALA MET CYS MET LEU VAL SEQRES 32 B 538 ALA ARG THR GLU LYS ASP SER HIS MET VAL ALA PHE SER SEQRES 33 B 538 ASP GLU MET LEU PRO CYS PRO ILE THR VAL ASN MET LEU SEQRES 34 B 538 LEU HIS GLU VAL VAL GLU LYS MET SER ASP ILE THR MET SEQRES 35 B 538 GLY SER THR ASP CYS ALA LEU PRO MET LEU TRP ALA GLN SEQRES 36 B 538 LYS THR ASN THR ALA ALA ASP ILE PHE ILE VAL PHE THR SEQRES 37 B 538 ASP CYS GLU THR ASN VAL GLU ASP VAL HIS PRO ALA THR SEQRES 38 B 538 ALA LEU LYS GLN TYR ARG GLU LYS MET GLY ILE PRO ALA SEQRES 39 B 538 LYS LEU ILE VAL CYS ALA MET THR SER ASN GLY PHE SER SEQRES 40 B 538 ILE ALA ASP PRO ASP ASP ARG GLY MET LEU ASP ILE CYS SEQRES 41 B 538 GLY PHE ASP SER GLY ALA LEU ASP VAL ILE ARG ASN PHE SEQRES 42 B 538 THR LEU ASP LEU ILE MODRES 1YVP IU C 3 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU D 1 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU D 2 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU D 6 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU E 3 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU F 1 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU F 2 U 5-IODOURIDINE-5'-MONOPHOSPHATE MODRES 1YVP IU F 6 U 5-IODOURIDINE-5'-MONOPHOSPHATE HET IU C 3 21 HET IU D 1 18 HET IU D 2 21 HET IU D 6 21 HET IU E 3 21 HET IU F 1 18 HET IU F 2 21 HET IU F 6 21 HET ACT A2001 4 HET MG A1001 1 HET ACT B2002 4 HET MG B1002 1 HETNAM IU 5-IODOURIDINE-5'-MONOPHOSPHATE HETNAM ACT ACETATE ION HETNAM MG MAGNESIUM ION FORMUL 1 IU 8(C9 H12 I N2 O9 P) FORMUL 9 ACT 2(C2 H3 O2 1-) FORMUL 10 MG 2(MG 2+) FORMUL 13 HOH *408(H2 O) HELIX 1 1 SER A 28 GLY A 40 1 13 HELIX 2 2 GLU A 49 ASP A 67 1 19 HELIX 3 3 LYS A 69 GLY A 84 1 16 HELIX 4 4 GLN A 89 SER A 100 1 12 HELIX 5 5 ASP A 104 CYS A 119 1 16 HELIX 6 6 ILE A 121 MET A 139 1 19 HELIX 7 7 GLY A 145 THR A 158 1 14 HELIX 8 8 ASP A 160 TYR A 171 1 12 HELIX 9 9 HIS A 179 HIS A 187 1 9 HELIX 10 10 ASN A 192 GLY A 205 1 14 HELIX 11 11 GLY A 205 TYR A 213 1 9 HELIX 12 12 SER A 219 VAL A 235 1 17 HELIX 13 13 LYS A 236 THR A 238 5 3 HELIX 14 14 ASP A 240 ARG A 252 1 13 HELIX 15 15 VAL A 254 LEU A 258 5 5 HELIX 16 16 THR A 260 LYS A 264 5 5 HELIX 17 17 SER A 265 ASP A 275 1 11 HELIX 18 18 PRO A 277 ASN A 284 1 8 HELIX 19 19 ASN A 284 ASP A 291 1 8 HELIX 20 20 SER A 298 THR A 309 1 12 HELIX 21 21 ASN A 310 ALA A 317 1 8 HELIX 22 22 HIS A 320 GLY A 334 1 15 HELIX 23 23 ASP A 346 PHE A 361 1 16 HELIX 24 24 SER A 378 GLN A 383 5 6 HELIX 25 25 ASN A 391 GLU A 407 1 17 HELIX 26 26 LEU A 429 LYS A 436 1 8 HELIX 27 27 ALA A 448 THR A 457 1 10 HELIX 28 28 HIS A 478 GLY A 491 1 14 HELIX 29 29 GLY A 525 LEU A 535 1 11 HELIX 30 30 SER B 28 GLY B 40 1 13 HELIX 31 31 GLU B 49 ASP B 67 1 19 HELIX 32 32 LYS B 69 GLU B 83 1 15 HELIX 33 33 GLN B 89 GLN B 101 1 13 HELIX 34 34 ASP B 104 CYS B 119 1 16 HELIX 35 35 ILE B 121 MET B 139 1 19 HELIX 36 36 GLY B 145 THR B 158 1 14 HELIX 37 37 ASP B 160 TYR B 171 1 12 HELIX 38 38 HIS B 179 HIS B 187 1 9 HELIX 39 39 ASN B 192 LYS B 204 1 13 HELIX 40 40 GLY B 205 TYR B 213 1 9 HELIX 41 41 GLU B 221 VAL B 235 1 15 HELIX 42 42 ASP B 240 ARG B 252 1 13 HELIX 43 43 VAL B 254 LEU B 258 5 5 HELIX 44 44 LEU B 259 LYS B 264 5 6 HELIX 45 45 SER B 265 GLN B 274 1 10 HELIX 46 46 PRO B 277 ASN B 284 1 8 HELIX 47 47 ASN B 284 ASP B 291 1 8 HELIX 48 48 SER B 298 THR B 309 1 12 HELIX 49 49 ASN B 310 ALA B 317 1 8 HELIX 50 50 HIS B 320 GLY B 334 1 15 HELIX 51 51 ASP B 346 SER B 360 1 15 HELIX 52 52 SER B 378 GLN B 383 5 6 HELIX 53 53 ASN B 391 GLU B 407 1 17 HELIX 54 54 LEU B 429 SER B 438 1 10 HELIX 55 55 ALA B 448 THR B 457 1 10 HELIX 56 56 HIS B 478 GLY B 491 1 14 HELIX 57 57 GLY B 525 LEU B 535 1 11 SHEET 1 A 3 VAL A 16 PRO A 17 0 SHEET 2 A 3 TYR A 23 GLN A 26 -1 O VAL A 24 N VAL A 16 SHEET 3 A 3 PHE A 506 SER A 507 -1 O SER A 507 N TRP A 25 SHEET 1 B 2 GLN A 173 ARG A 174 0 SHEET 2 B 2 TRP A 177 SER A 178 -1 O TRP A 177 N ARG A 174 SHEET 1 C 6 MET A 419 LEU A 420 0 SHEET 2 C 6 SER A 410 PHE A 415 -1 N ALA A 414 O LEU A 420 SHEET 3 C 6 PHE A 371 ASP A 376 1 N LEU A 373 O HIS A 411 SHEET 4 C 6 ILE A 463 THR A 468 1 O ILE A 463 N LEU A 372 SHEET 5 C 6 LYS A 495 ALA A 500 1 O ILE A 497 N PHE A 464 SHEET 6 C 6 MET A 516 CYS A 520 1 O LEU A 517 N VAL A 498 SHEET 1 D 3 VAL B 16 PRO B 17 0 SHEET 2 D 3 TYR B 23 GLN B 26 -1 O VAL B 24 N VAL B 16 SHEET 3 D 3 PHE B 506 SER B 507 -1 O SER B 507 N TRP B 25 SHEET 1 E 2 GLN B 173 ARG B 174 0 SHEET 2 E 2 TRP B 177 SER B 178 -1 O TRP B 177 N ARG B 174 SHEET 1 F 6 MET B 419 LEU B 420 0 SHEET 2 F 6 SER B 410 PHE B 415 -1 N ALA B 414 O LEU B 420 SHEET 3 F 6 PHE B 371 ASP B 376 1 N LEU B 373 O VAL B 413 SHEET 4 F 6 ILE B 463 THR B 468 1 O ILE B 465 N ALA B 374 SHEET 5 F 6 LYS B 495 ALA B 500 1 O ILE B 497 N PHE B 464 SHEET 6 F 6 MET B 516 CYS B 520 1 O LEU B 517 N VAL B 498 LINK O3' C C 2 P IU C 3 1555 1555 1.62 LINK O3' IU C 3 P G C 4 1555 1555 1.61 LINK O3' IU D 1 P IU D 2 1555 1555 1.61 LINK O3' IU D 2 P G D 3 1555 1555 1.60 LINK O3' C D 5 P IU D 6 1555 1555 1.61 LINK O3' IU D 6 P A D 7 1555 1555 1.61 LINK O3' C E 2 P IU E 3 1555 1555 1.61 LINK O3' IU E 3 P G E 4 1555 1555 1.61 LINK O3' IU F 1 P IU F 2 1555 1555 1.61 LINK O3' IU F 2 P G F 3 1555 1555 1.61 LINK O3' C F 5 P IU F 6 1555 1555 1.61 LINK O3' IU F 6 P A F 7 1555 1555 1.61 LINK OG SER A 378 MG MG A1001 1555 1555 2.20 LINK OG SER A 380 MG MG A1001 1555 1555 2.19 LINK OG1 THR A 445 MG MG A1001 1555 1555 2.19 LINK MG MG A1001 OXT ACT A2001 1555 1555 1.84 LINK MG MG A1001 O HOH A2167 1555 1555 2.04 LINK MG MG A1001 O HOH A2168 1555 1555 2.02 LINK OG SER B 378 MG MG B1002 1555 1555 2.14 LINK OG SER B 380 MG MG B1002 1555 1555 2.06 LINK OG1 THR B 445 MG MG B1002 1555 1555 2.16 LINK MG MG B1002 OXT ACT B2002 1555 1555 1.84 LINK MG MG B1002 O HOH B2170 1555 1555 2.04 LINK MG MG B1002 O HOH B2171 1555 1555 2.02 SITE 1 AC1 9 TYR A 47 SER A 378 ALA A 379 SER A 380 SITE 2 AC1 9 GLY A 443 SER A 444 THR A 445 ASN A 473 SITE 3 AC1 9 MG A1001 SITE 1 AC2 10 TYR B 47 SER B 378 ALA B 379 SER B 380 SITE 2 AC2 10 GLY B 443 SER B 444 THR B 445 ASN B 473 SITE 3 AC2 10 MG B1002 HOH B2072 SITE 1 AC3 6 SER A 378 SER A 380 THR A 445 ACT A2001 SITE 2 AC3 6 HOH A2167 HOH A2168 SITE 1 AC4 6 SER B 378 SER B 380 THR B 445 ACT B2002 SITE 2 AC4 6 HOH B2170 HOH B2171 CRYST1 60.300 153.650 80.560 90.00 92.80 90.00 P 1 21 1 8 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 0.016584 0.000000 0.000811 0.00000 SCALE2 0.000000 0.006508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012428 0.00000