HEADER TRANSCRIPTION 26-DEC-19 6LMS TITLE SOLUTION NMR STRUCTURE COLD SHOCK DOMAIN OF YB1 FROM HOMO SAPIENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: Y-BOX-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YB-1,CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A,CBF-A, COMPND 5 DNA-BINDING PROTEIN B,DBPB,ENHANCER FACTOR I SUBUNIT A,EFI-A, COMPND 6 NUCLEASE-SENSITIVE ELEMENT-BINDING PROTEIN 1,Y-BOX TRANSCRIPTION COMPND 7 FACTOR; COMPND 8 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CSD, TRANSCRIPTION, DNA BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.LI,J.ZHANG,Y.YANG REVDAT 3 14-JUN-23 6LMS 1 REMARK REVDAT 2 17-FEB-21 6LMS 1 JRNL REVDAT 1 22-JUL-20 6LMS 0 JRNL AUTH J.ZHANG,J.S.FAN,S.LI,Y.YANG,P.SUN,Q.ZHU,J.WANG,B.JIANG, JRNL AUTH 2 D.YANG,M.LIU JRNL TITL STRUCTURAL BASIS OF DNA BINDING TO HUMAN YB-1 COLD SHOCK JRNL TITL 2 DOMAIN REGULATED BY PHOSPHORYLATION. JRNL REF NUCLEIC ACIDS RES. V. 48 9361 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32710623 JRNL DOI 10.1093/NAR/GKAA619 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EEFX FORCE-FIELD REMARK 4 REMARK 4 6LMS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300015074. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 YB1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D C(CO)NH; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRPIPE, NMRFAM-SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 35 REMARK 465 HIS A 36 REMARK 465 HIS A 37 REMARK 465 HIS A 38 REMARK 465 HIS A 39 REMARK 465 HIS A 40 REMARK 465 HIS A 41 REMARK 465 SER A 42 REMARK 465 SER A 43 REMARK 465 GLY A 44 REMARK 465 LEU A 45 REMARK 465 VAL A 46 REMARK 465 PRO A 47 REMARK 465 ARG A 48 REMARK 465 GLY A 49 REMARK 465 SER A 50 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 LYS A 52 -173.98 64.74 REMARK 500 1 LYS A 58 108.09 -42.19 REMARK 500 2 LYS A 58 105.92 -43.04 REMARK 500 2 SER A 136 -163.70 -118.04 REMARK 500 3 LYS A 58 105.73 -46.30 REMARK 500 4 LYS A 58 105.44 -44.34 REMARK 500 5 LYS A 58 104.70 -47.76 REMARK 500 6 LYS A 58 107.46 -44.33 REMARK 500 7 LYS A 58 107.08 -50.85 REMARK 500 7 LYS A 118 31.60 -140.93 REMARK 500 8 LYS A 52 -170.11 66.37 REMARK 500 8 LYS A 58 104.27 -36.87 REMARK 500 9 LYS A 58 104.44 -47.72 REMARK 500 10 LYS A 58 107.33 -46.25 REMARK 500 11 LYS A 58 106.15 -42.34 REMARK 500 12 LYS A 52 -155.16 -152.45 REMARK 500 12 LYS A 58 107.74 -45.65 REMARK 500 12 SER A 136 -168.58 -119.17 REMARK 500 13 LYS A 58 105.92 -41.98 REMARK 500 14 LYS A 58 106.49 -44.55 REMARK 500 15 LYS A 58 106.17 -44.51 REMARK 500 16 LYS A 58 108.25 -44.48 REMARK 500 17 LYS A 58 107.09 -42.93 REMARK 500 18 LYS A 52 -169.49 66.13 REMARK 500 18 LYS A 58 106.39 -45.02 REMARK 500 18 TRP A 65 148.83 -171.58 REMARK 500 18 SER A 136 -165.39 -102.87 REMARK 500 19 LYS A 58 104.91 -43.56 REMARK 500 19 THR A 80 -8.57 -141.83 REMARK 500 19 ASP A 83 133.74 74.83 REMARK 500 20 LYS A 58 106.26 -46.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36307 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE COLD SHOCK DOMAIN OF YB1 FROM HOMO SAPIENS DBREF 6LMS A 51 140 UNP P67809 YBOX1_HUMAN 51 140 SEQADV 6LMS MET A 35 UNP P67809 INITIATING METHIONINE SEQADV 6LMS HIS A 36 UNP P67809 EXPRESSION TAG SEQADV 6LMS HIS A 37 UNP P67809 EXPRESSION TAG SEQADV 6LMS HIS A 38 UNP P67809 EXPRESSION TAG SEQADV 6LMS HIS A 39 UNP P67809 EXPRESSION TAG SEQADV 6LMS HIS A 40 UNP P67809 EXPRESSION TAG SEQADV 6LMS HIS A 41 UNP P67809 EXPRESSION TAG SEQADV 6LMS SER A 42 UNP P67809 EXPRESSION TAG SEQADV 6LMS SER A 43 UNP P67809 EXPRESSION TAG SEQADV 6LMS GLY A 44 UNP P67809 EXPRESSION TAG SEQADV 6LMS LEU A 45 UNP P67809 EXPRESSION TAG SEQADV 6LMS VAL A 46 UNP P67809 EXPRESSION TAG SEQADV 6LMS PRO A 47 UNP P67809 EXPRESSION TAG SEQADV 6LMS ARG A 48 UNP P67809 EXPRESSION TAG SEQADV 6LMS GLY A 49 UNP P67809 EXPRESSION TAG SEQADV 6LMS SER A 50 UNP P67809 EXPRESSION TAG SEQRES 1 A 106 MET HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 A 106 ARG GLY SER ASP LYS LYS VAL ILE ALA THR LYS VAL LEU SEQRES 3 A 106 GLY THR VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY SEQRES 4 A 106 PHE ILE ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL SEQRES 5 A 106 HIS GLN THR ALA ILE LYS LYS ASN ASN PRO ARG LYS TYR SEQRES 6 A 106 LEU ARG SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP SEQRES 7 A 106 VAL VAL GLU GLY GLU LYS GLY ALA GLU ALA ALA ASN VAL SEQRES 8 A 106 THR GLY PRO GLY GLY VAL PRO VAL GLN GLY SER LYS TYR SEQRES 9 A 106 ALA ALA HELIX 1 AA1 THR A 89 ILE A 91 5 3 HELIX 2 AA2 GLY A 127 VAL A 131 5 5 SHEET 1 AA1 6 VAL A 54 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 VAL A 114 O GLU A 121 SHEET 6 AA1 6 VAL A 54 ASN A 67 -1 N VAL A 59 O PHE A 111 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 MODEL 1