HEADER GENE REGULATION 14-MAY-14 4PKD TITLE U1-70K IN COMPLEX WITH U1 SNRNA STEM-LOOPS 1 AND U1-A RRM IN COMPLEX TITLE 2 WITH STEM-LOOP 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: U1 SNRNA STEM-LOOPS 1 AND 2 (55-MER); COMPND 3 CHAIN: V; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RNA IS A DUMBELL-SHAPED FUSION OF U1 SNRNA STEM-LOOP 1 COMPND 6 AND THE APICAL PART OF U1 SNRNA STEM-LOOP 2 JOINED BY A 3 BASE PAIR COMPND 7 LINKER. TRANSCRIBED BY T7 RNA POLYMERASE FROM A LINEARISED PLASMID COMPND 8 TEMPLATE.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A,U1 SMALL NUCLEAR COMPND 11 RIBONUCLEOPROTEIN 70 KDA; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: U1A,SNRNP70; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 OTHER_DETAILS: BOTH THIS PROTEIN AND U1-70K ARE EXPRESSED TOGETHER AS COMPND 17 A FUSION PROTEIN. THE C-TERMINUS OF U1-A AND THE LINKER PEPTIDE ARE COMPND 18 DISORDERED IN THE STRUCTURE. THE TWO PROTEINS HAVE BEEN GIVEN COMPND 19 SEPARATE CHAIN IDENTIFIERS SO THAT THEIR NORMAL NUMBERING IS COMPND 20 PRESERVED., U1-A AND THIS PROTEIN ARE EXPRESSED TOGETHER AS A FUSION COMPND 21 PROTEIN. THE C-TERMINUS OF U1-A AND THE LINKER PEPTIDE ARE DISORDERED COMPND 22 IN THE STRUCTURE. THE TWO PROTEINS HAVE BEEN GIVEN SEPARATE CHAIN COMPND 23 IDENTIFIERS SO THAT THEIR NORMAL NUMBERING IS PRESERVED. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: SEE COMPOUND DETAILS.; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SUS SCROFA, HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: PIG, HUMAN; SOURCE 10 ORGANISM_TAXID: 9823, 9606; SOURCE 11 GENE: SNRPA, SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: PLYSS; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET13 KEYWDS U1-70K, U1 SNRNP, PRE-MRNA SPLICING, SPLICEOSOME, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.OUBRIDGE,Y.KONDO,A.M.VAN ROON,K.NAGAI REVDAT 3 20-DEC-23 4PKD 1 LINK REVDAT 2 14-JAN-15 4PKD 1 JRNL REVDAT 1 31-DEC-14 4PKD 0 JRNL AUTH Y.KONDO,C.OUBRIDGE,A.M.VAN ROON,K.NAGAI JRNL TITL CRYSTAL STRUCTURE OF HUMAN U1 SNRNP, A SMALL NUCLEAR JRNL TITL 2 RIBONUCLEOPROTEIN PARTICLE, REVEALS THE MECHANISM OF 5' JRNL TITL 3 SPLICE SITE RECOGNITION. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 25555158 JRNL DOI 10.7554/ELIFE.04986 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.A.POMERANZ KRUMMEL,C.OUBRIDGE,A.K.LEUNG,J.LI,K.NAGAI REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN SPLICEOSOMAL U1 SNRNP AT 5.5 A REMARK 1 TITL 2 RESOLUTION. REMARK 1 REF NATURE V. 458 475 2009 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 19325628 REMARK 1 DOI 10.1038/NATURE07851 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.OUBRIDGE,N.ITO,P.R.EVANS,C.H.TEO,K.NAGAI REMARK 1 TITL CRYSTAL STRUCTURE AT 1.92 A RESOLUTION OF THE RNA-BINDING REMARK 1 TITL 2 DOMAIN OF THE U1A SPLICEOSOMAL PROTEIN COMPLEXED WITH AN RNA REMARK 1 TITL 3 HAIRPIN. REMARK 1 REF NATURE V. 372 432 1994 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 7984237 REMARK 1 DOI 10.1038/372432A0 REMARK 1 REFERENCE 3 REMARK 1 AUTH G.WEBER,S.TROWITZSCH,B.KASTNER,R.LUHRMANN,M.C.WAHL REMARK 1 TITL FUNCTIONAL ORGANIZATION OF THE SM CORE IN THE CRYSTAL REMARK 1 TITL 2 STRUCTURE OF HUMAN U1 SNRNP. REMARK 1 REF EMBO J. V. 29 4172 2010 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 21113136 REMARK 1 DOI 10.1038/EMBOJ.2010.295 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 15156 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 + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 812 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1097 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.4430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1954 REMARK 3 NUCLEIC ACID ATOMS : 1177 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.18000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -2.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.618 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.404 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3309 ; 0.019 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 2465 ; 0.013 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4715 ; 1.910 ; 1.688 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5722 ; 3.142 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 238 ; 6.870 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;32.277 ;22.059 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 377 ;19.723 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.822 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2886 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 788 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 958 ; 2.735 ; 4.543 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 957 ; 2.735 ; 4.543 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1194 ; 4.168 ; 6.800 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1195 ; 4.166 ; 6.800 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2351 ; 3.636 ; 5.526 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2352 ; 3.635 ; 5.526 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3522 ; 5.608 ; 8.238 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14367 ; 8.964 ;50.304 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14368 ; 8.963 ;50.306 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4PKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201558. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15967 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 87.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1URN REMARK 200 REMARK 200 REMARK: SIX-SIDED PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% MPD, 0.15 M SODIUM CHLORIDE, 0.1 M REMARK 280 SODIUM ACETATE, PH 4.2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.11000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.11000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.30000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: V, 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 GLY B 2 REMARK 465 VAL B 3 REMARK 465 PRO B 4 REMARK 465 GLU B 5 REMARK 465 ARG B 104 REMARK 465 ASP B 105 REMARK 465 ARG B 106 REMARK 465 LYS B 107 REMARK 465 ARG B 108 REMARK 465 GLU B 109 REMARK 465 LYS B 110 REMARK 465 ARG B 111 REMARK 465 GLY B 112 REMARK 465 SER B 113 REMARK 465 GLY B 114 REMARK 465 SER B 115 REMARK 465 GLY B 116 REMARK 465 SER B 117 REMARK 465 GLY B 118 REMARK 465 SER B 119 REMARK 465 GLY B 120 REMARK 465 SER B 121 REMARK 465 GLY B 122 REMARK 465 SER B 123 REMARK 465 GLY B 124 REMARK 465 ALA B 125 REMARK 465 GLY B 268 REMARK 465 ALA B 269 REMARK 465 ASP B 270 REMARK 465 VAL B 271 REMARK 465 ASN B 272 REMARK 465 ILE B 273 REMARK 465 ARG B 274 REMARK 465 HIS B 275 REMARK 465 SER B 276 REMARK 465 GLY B 277 REMARK 465 ARG B 278 REMARK 465 ASP B 279 REMARK 465 ASP B 280 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 LYS B 20 CD CE NZ REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 VAL B 102 CG1 CG2 REMARK 470 GLU B 126 CG CD OE1 OE2 REMARK 470 ARG B 128 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 131 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 141 CG CD OE1 OE2 REMARK 470 LYS B 207 CG CD CE NZ 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 V 100 O3' A V 101 P -0.088 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 U V 67 O5' - P - OP2 ANGL. DEV. = -6.8 DEGREES REMARK 500 C V 79 O5' - P - OP1 ANGL. DEV. = 11.5 DEGREES REMARK 500 A V 100 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 G V 102 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 186 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 209 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B 230 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG B 255 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 256 CG - CD - NE ANGL. DEV. = -13.8 DEGREES REMARK 500 ARG B 256 NE - CZ - NH2 ANGL. DEV. = -3.9 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 PRO B 8 152.58 -45.33 REMARK 500 ARG B 204 -72.04 -89.49 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 V 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U V 92 O4 REMARK 620 2 G V 103 O6 88.9 REMARK 620 3 HOH V 314 O 130.7 117.9 REMARK 620 4 HOH V 318 O 76.5 77.3 71.2 REMARK 620 5 HOH V 319 O 68.1 150.8 70.3 79.8 REMARK 620 6 HOH V 329 O 73.5 120.5 116.2 144.4 71.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG V 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U V 92 O4 REMARK 620 2 HOH V 317 O 91.6 REMARK 620 3 HOH V 319 O 77.7 165.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH V 308 O REMARK 620 2 HOH V 310 O 110.2 REMARK 620 3 TRP B 154 O 80.8 160.8 REMARK 620 4 HOH B 420 O 96.6 101.9 92.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG V 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG V 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CW1 RELATED DB: PDB REMARK 900 5.5 A STRUCTURE OF RECOMBINANT U1 SNRNP, WHICH CONTAINS U1-70K RRM REMARK 900 AND HELIX 0 BOUND TO STEM-LOOP 1. REMARK 900 RELATED ID: 1URN RELATED DB: PDB REMARK 900 U1-A PROTEIN IN COMPLEX WITH STEM-LOOP 2 RNA. REMARK 900 RELATED ID: 3PGW RELATED DB: PDB REMARK 900 4.4 A STRUCTURE OF NATIVE, PROTEASE-TREATED U1 SNRNP, WHICH REMARK 900 CONTAINS U1-70K RRM AND HELIX 0 BOUND TO STEM-LOOP 1. DBREF 4PKD V 59 113 PDB 4PKD 4PKD 59 113 DBREF 4PKD B 2 111 UNP Q06AA4 SNRPA_PIG 2 111 DBREF 4PKD B 125 280 UNP P08621 RU17_HUMAN 60 215 SEQADV 4PKD GLY B 2 UNP Q06AA4 ALA 2 ENGINEERED MUTATION SEQADV 4PKD GLY B 112 UNP Q06AA4 LINKER SEQADV 4PKD SER B 113 UNP Q06AA4 LINKER SEQADV 4PKD GLY B 114 UNP Q06AA4 LINKER SEQADV 4PKD SER B 115 UNP Q06AA4 LINKER SEQADV 4PKD GLY B 116 UNP Q06AA4 LINKER SEQADV 4PKD SER B 117 UNP Q06AA4 LINKER SEQADV 4PKD GLY B 118 UNP Q06AA4 LINKER SEQADV 4PKD SER B 119 UNP Q06AA4 LINKER SEQADV 4PKD GLY B 120 UNP Q06AA4 LINKER SEQADV 4PKD SER B 121 UNP Q06AA4 LINKER SEQADV 4PKD GLY B 122 UNP Q06AA4 LINKER SEQADV 4PKD SER B 123 UNP Q06AA4 LINKER SEQADV 4PKD GLY B 124 UNP Q06AA4 LINKER SEQRES 1 V 55 GTP G A U C C A U U G C A C SEQRES 2 V 55 U C C G G A U C C A G G A SEQRES 3 V 55 G A U A C C A U G A U C A SEQRES 4 V 55 C G A A G G U G G U U U U SEQRES 5 V 55 C C U SEQRES 1 B 279 GLY VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR ILE SEQRES 2 B 279 ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU LYS SEQRES 3 B 279 LYS SER LEU TYR ALA ILE PHE SER GLN PHE GLY GLN ILE SEQRES 4 B 279 LEU ASP ILE LEU VAL SER ARG SER LEU LYS MET ARG GLY SEQRES 5 B 279 GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA THR SEQRES 6 B 279 ASN ALA LEU ARG SER MET GLN GLY PHE PRO PHE TYR ASP SEQRES 7 B 279 LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER ASP SEQRES 8 B 279 ILE ILE ALA LYS MET LYS GLY THR PHE VAL GLU ARG ASP SEQRES 9 B 279 ARG LYS ARG GLU LYS ARG GLY SER GLY SER GLY SER GLY SEQRES 10 B 279 SER GLY SER GLY SER GLY ALA GLU THR ARG GLU GLU ARG SEQRES 11 B 279 MET GLU ARG LYS ARG ARG GLU LYS ILE GLU ARG ARG GLN SEQRES 12 B 279 GLN GLU VAL GLU THR GLU LEU LYS MET TRP ASP PRO HIS SEQRES 13 B 279 ASN ASP PRO ASN ALA GLN GLY ASP ALA PHE LYS THR LEU SEQRES 14 B 279 PHE VAL ALA ARG VAL ASN TYR ASP THR THR GLU SER LYS SEQRES 15 B 279 LEU ARG ARG GLU PHE GLU VAL TYR GLY PRO ILE LYS ARG SEQRES 16 B 279 ILE HIS MET VAL TYR SER LYS ARG SER GLY LYS PRO ARG SEQRES 17 B 279 GLY TYR ALA PHE ILE GLU TYR GLU HIS GLU ARG ASP MET SEQRES 18 B 279 HIS SER ALA TYR LYS HIS ALA ASP GLY LYS LYS ILE ASP SEQRES 19 B 279 GLY ARG ARG VAL LEU VAL ASP VAL GLU ARG GLY ARG THR SEQRES 20 B 279 VAL LYS GLY TRP ARG PRO ARG ARG LEU GLY GLY GLY LEU SEQRES 21 B 279 GLY GLY THR ARG ARG GLY GLY ALA ASP VAL ASN ILE ARG SEQRES 22 B 279 HIS SER GLY ARG ASP ASP HET GTP V 59 32 HET MG V 201 1 HET MG V 202 1 HET MG B 301 1 HET IMD B 302 5 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM IMD IMIDAZOLE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 3 MG 3(MG 2+) FORMUL 6 IMD C3 H5 N2 1+ FORMUL 7 HOH *113(H2 O) HELIX 1 AA1 LYS B 22 GLN B 36 1 15 HELIX 2 AA2 GLU B 61 GLN B 73 1 13 HELIX 3 AA3 SER B 91 LYS B 98 1 8 HELIX 4 AA4 THR B 127 LYS B 152 1 26 HELIX 5 AA5 MET B 153 TRP B 154 5 2 HELIX 6 AA6 ASP B 155 ASP B 159 5 5 HELIX 7 AA7 ASP B 165 PHE B 167 5 3 HELIX 8 AA8 THR B 180 VAL B 190 1 11 HELIX 9 AA9 HIS B 218 ALA B 229 1 12 HELIX 10 AB1 PRO B 254 GLY B 258 5 5 SHEET 1 AA1 4 ILE B 40 VAL B 45 0 SHEET 2 AA1 4 ALA B 55 PHE B 59 -1 O ILE B 58 N ASP B 42 SHEET 3 AA1 4 THR B 11 ASN B 15 -1 N ILE B 14 O ALA B 55 SHEET 4 AA1 4 ARG B 83 TYR B 86 -1 O GLN B 85 N TYR B 13 SHEET 1 AA2 4 ILE B 194 TYR B 201 0 SHEET 2 AA2 4 PRO B 208 TYR B 216 -1 O ARG B 209 N VAL B 200 SHEET 3 AA2 4 THR B 169 ALA B 173 -1 N LEU B 170 O ILE B 214 SHEET 4 AA2 4 LEU B 240 VAL B 243 -1 O ASP B 242 N PHE B 171 SHEET 1 AA3 2 LYS B 233 ILE B 234 0 SHEET 2 AA3 2 ARG B 237 ARG B 238 -1 O ARG B 237 N ILE B 234 LINK O3' GTP V 59 P G V 60 1555 1555 1.59 LINK O4 U V 92 MG MG V 201 1555 1555 2.86 LINK O4 U V 92 MG MG V 202 1555 1555 2.76 LINK O6 G V 103 MG MG V 201 1555 1555 2.80 LINK MG MG V 201 O HOH V 314 1555 1555 2.62 LINK MG MG V 201 O HOH V 318 1555 1555 2.81 LINK MG MG V 201 O HOH V 319 1555 1555 2.94 LINK MG MG V 201 O HOH V 329 1555 1555 2.56 LINK MG MG V 202 O HOH V 317 1555 1555 2.55 LINK MG MG V 202 O HOH V 319 1555 1555 2.40 LINK O HOH V 308 MG MG B 301 4548 1555 2.37 LINK O HOH V 310 MG MG B 301 4548 1555 2.37 LINK O TRP B 154 MG MG B 301 1555 1555 2.57 LINK MG MG B 301 O HOH B 420 1555 1555 2.07 SITE 1 AC1 7 A V 91 U V 92 G V 103 HOH V 314 SITE 2 AC1 7 HOH V 318 HOH V 319 HOH V 329 SITE 1 AC2 3 U V 92 HOH V 317 HOH V 319 SITE 1 AC3 3 LEU B 151 TRP B 154 HOH B 420 SITE 1 AC4 3 ASP B 92 C V 71 U V 72 CRYST1 80.220 66.600 93.730 90.00 110.95 90.00 C 1 2 1 4 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 0.012466 0.000000 0.004773 0.00000 SCALE2 0.000000 0.015015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011424 0.00000 HETATM 1 PG GTP V 59 -56.082 10.426 90.269 1.00128.50 P HETATM 2 O1G GTP V 59 -57.304 9.526 90.172 1.00126.66 O HETATM 3 O2G GTP V 59 -55.288 10.581 89.001 1.00121.03 O HETATM 4 O3G GTP V 59 -56.262 11.757 90.912 1.00124.80 O HETATM 5 O3B GTP V 59 -55.148 9.561 91.247 1.00130.04 O HETATM 6 PB GTP V 59 -53.592 9.915 91.425 1.00131.95 P HETATM 7 O1B GTP V 59 -53.276 11.153 90.578 1.00127.21 O HETATM 8 O2B GTP V 59 -52.848 8.625 91.249 1.00119.30 O HETATM 9 O3A GTP V 59 -53.569 10.241 93.002 1.00118.69 O HETATM 10 PA GTP V 59 -53.749 11.763 93.485 1.00115.75 P HETATM 11 O1A GTP V 59 -52.430 12.305 93.987 1.00115.45 O HETATM 12 O2A GTP V 59 -54.415 12.617 92.448 1.00115.97 O HETATM 13 O5' GTP V 59 -54.762 11.517 94.674 1.00105.00 O HETATM 14 C5' GTP V 59 -56.149 11.624 94.476 1.00 98.01 C HETATM 15 C4' GTP V 59 -56.824 11.568 95.832 1.00 97.39 C HETATM 16 O4' GTP V 59 -56.054 10.821 96.809 1.00 98.48 O HETATM 17 C3' GTP V 59 -57.003 12.960 96.389 1.00 95.66 C HETATM 18 O3' GTP V 59 -58.234 13.515 95.976 1.00100.00 O HETATM 19 C2' GTP V 59 -56.949 12.755 97.858 1.00 94.76 C HETATM 20 O2' GTP V 59 -58.188 12.510 98.432 1.00 89.31 O HETATM 21 C1' GTP V 59 -55.992 11.543 98.046 1.00 94.34 C HETATM 22 N9 GTP V 59 -54.648 12.102 98.311 1.00 85.87 N HETATM 23 C8 GTP V 59 -53.522 11.880 97.660 1.00 81.72 C HETATM 24 N7 GTP V 59 -52.521 12.602 98.183 1.00 78.62 N HETATM 25 C5 GTP V 59 -52.978 13.321 99.177 1.00 76.05 C HETATM 26 C6 GTP V 59 -52.454 14.290 100.178 1.00 76.51 C HETATM 27 O6 GTP V 59 -51.264 14.646 100.182 1.00 73.92 O HETATM 28 N1 GTP V 59 -53.331 14.800 101.069 1.00 76.58 N HETATM 29 C2 GTP V 59 -54.638 14.446 101.070 1.00 73.03 C HETATM 30 N2 GTP V 59 -55.470 14.968 101.962 1.00 70.37 N HETATM 31 N3 GTP V 59 -55.174 13.570 100.200 1.00 74.72 N HETATM 32 C4 GTP V 59 -54.396 12.978 99.259 1.00 80.30 C