HEADER RNA BINDING PROTEIN/RNA 20-NOV-17 5YTT TITLE CRYSTAL STRUCTURE OF YB1 COLD-SHOCK DOMAIN IN COMPLEX WITH UCAUGU COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEASE-SENSITIVE ELEMENT-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A,CBF-A,DNA- COMPND 5 BINDING PROTEIN B,DBPB,ENHANCER FACTOR I SUBUNIT A,EFI-A,Y-BOX COMPND 6 TRANSCRIPTION FACTOR,Y-BOX-BINDING PROTEIN 1,YB-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(P*UP*CP*AP*UP*GP*U)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: YBX1, NSEP1, YB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS YB1, COLD-SHOCK DOMAIN, CAUG, RNA BINDING PROTEIN, RNA BINDING KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.YANG,Y.HUANG REVDAT 4 22-NOV-23 5YTT 1 REMARK REVDAT 3 24-JUL-19 5YTT 1 JRNL REVDAT 2 19-JUN-19 5YTT 1 JRNL REVDAT 1 05-DEC-18 5YTT 0 JRNL AUTH X.J.YANG,H.ZHU,S.R.MU,W.J.WEI,X.YUAN,M.WANG,Y.LIU,J.HUI, JRNL AUTH 2 Y.HUANG JRNL TITL CRYSTAL STRUCTURE OF A Y-BOX BINDING PROTEIN 1 (YB-1)-RNA JRNL TITL 2 COMPLEX REVEALS KEY FEATURES AND RESIDUES INTERACTING WITH JRNL TITL 3 RNA. JRNL REF J.BIOL.CHEM. V. 294 10998 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31160337 JRNL DOI 10.1074/JBC.RA119.007545 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 46.6 REMARK 3 NUMBER OF REFLECTIONS : 10965 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1101 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.5441 - 3.1930 0.61 1616 182 0.1782 0.2371 REMARK 3 2 3.1930 - 2.5347 0.56 1497 162 0.1980 0.2260 REMARK 3 3 2.5347 - 2.2144 0.52 1360 154 0.1744 0.1919 REMARK 3 4 2.2144 - 2.0120 0.51 1356 152 0.1712 0.1782 REMARK 3 5 2.0120 - 1.8678 0.48 1290 140 0.1730 0.2126 REMARK 3 6 1.8678 - 1.7577 0.41 1073 124 0.1835 0.1993 REMARK 3 7 1.7577 - 1.6697 0.35 913 103 0.1960 0.2881 REMARK 3 8 1.6697 - 1.5970 0.28 759 84 0.2267 0.2031 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.640 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 776 REMARK 3 ANGLE : 1.072 1082 REMARK 3 CHIRALITY : 0.045 131 REMARK 3 PLANARITY : 0.005 117 REMARK 3 DIHEDRAL : 14.940 304 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -6.2485 23.1717 36.1764 REMARK 3 T TENSOR REMARK 3 T11: 0.0461 T22: 0.0806 REMARK 3 T33: 0.0923 T12: -0.0187 REMARK 3 T13: 0.0274 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 3.1957 L22: 2.3306 REMARK 3 L33: 1.6701 L12: 0.3045 REMARK 3 L13: -0.4893 L23: -0.3600 REMARK 3 S TENSOR REMARK 3 S11: -0.0790 S12: 0.0819 S13: -0.3140 REMARK 3 S21: -0.0379 S22: -0.0020 S23: -0.0518 REMARK 3 S31: 0.2126 S32: -0.0960 S33: 0.0147 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97852 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3PF5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % (V/V) 2-METHYL-2,4-PENTANEDIOL, REMARK 280 0.1 M SODIUM ACETATE, PH 4.5, 25 % (W/V) PEG 1500, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.05333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.02667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.05333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 12.02667 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 APPLY THE FOLLOWING TO CHAINS: A, 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 A 48 REMARK 465 SER A 49 REMARK 465 GLY A 50 REMARK 465 ASP A 51 REMARK 465 ASN A 95 REMARK 465 PRO A 96 REMARK 465 ARG A 97 REMARK 465 GLY A 130 REMARK 465 U B 6 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 353 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A 354 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A 355 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH A 356 DISTANCE = 9.99 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5YTS RELATED DB: PDB REMARK 900 RELATED ID: 5YTV RELATED DB: PDB REMARK 900 RELATED ID: 5YTX RELATED DB: PDB DBREF 5YTT A 50 130 UNP P67809 YBOX1_HUMAN 50 130 DBREF 5YTT B 1 7 PDB 5YTT 5YTT 1 7 SEQADV 5YTT GLY A 48 UNP P67809 EXPRESSION TAG SEQADV 5YTT SER A 49 UNP P67809 EXPRESSION TAG SEQRES 1 A 83 GLY SER GLY ASP LYS LYS VAL ILE ALA THR LYS VAL LEU SEQRES 2 A 83 GLY THR VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY SEQRES 3 A 83 PHE ILE ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL SEQRES 4 A 83 HIS GLN THR ALA ILE LYS LYS ASN ASN PRO ARG LYS TYR SEQRES 5 A 83 LEU ARG SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP SEQRES 6 A 83 VAL VAL GLU GLY GLU LYS GLY ALA GLU ALA ALA ASN VAL SEQRES 7 A 83 THR GLY PRO GLY GLY SEQRES 1 B 7 U C A U G U U HET SO4 A 201 5 HET SO4 A 202 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *62(H2 O) HELIX 1 AA1 THR A 89 ILE A 91 5 3 SHEET 1 AA1 6 LYS A 53 ASN A 67 0 SHEET 2 AA1 6 TYR A 72 ARG A 77 -1 O ASN A 76 N THR A 62 SHEET 3 AA1 6 ASP A 83 HIS A 87 -1 O VAL A 84 N ILE A 75 SHEET 4 AA1 6 GLY A 119 THR A 126 1 O ALA A 122 N PHE A 85 SHEET 5 AA1 6 THR A 108 GLY A 116 -1 N ASP A 112 O ALA A 123 SHEET 6 AA1 6 LYS A 53 ASN A 67 -1 N ILE A 55 O VAL A 113 SITE 1 AC1 5 LYS A 52 LYS A 53 VAL A 54 ARG A 101 SITE 2 AC1 5 SO4 A 202 SITE 1 AC2 4 LYS A 92 LYS A 93 ARG A 101 SO4 A 201 CRYST1 66.218 66.218 36.080 90.00 90.00 120.00 P 62 6 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 0.015102 0.008719 0.000000 0.00000 SCALE2 0.000000 0.017438 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027716 0.00000