HEADER DNA BINDING PROTEIN 26-DEC-19 6LMR TITLE SOLUTION STRUCTURE OF COLD SHOCK DOMAIN AND SSDNA COMPLEX 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; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(P*AP*AP*CP*AP*CP*CP*T)-3'); COMPND 11 CHAIN: B; COMPND 12 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS Y-BOX, COLD SHOCK DOMAIN, SSNDA, COMPLEX, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.FAN,D.YANG REVDAT 3 15-MAY-24 6LMR 1 REMARK REVDAT 2 02-FEB-22 6LMR 1 JRNL REVDAT 1 22-JUL-20 6LMR 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: NULL REMARK 4 REMARK 4 6LMR 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_1300015081. 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 : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 CSD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HCCH-TOCSY; 4D NOESY; 3D REMARK 210 FILTERED NOEST; 2D 13C/15N REMARK 210 FILTERED TOCSY; 2D 13C/15N REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, SPARKY, X-PLOR REMARK 210 NIH 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: 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. (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 28 REMARK 465 HIS A 29 REMARK 465 HIS A 30 REMARK 465 HIS A 31 REMARK 465 HIS A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 GLY A 35 REMARK 465 GLY A 36 REMARK 465 GLY A 37 REMARK 465 GLY A 38 REMARK 465 GLY A 39 REMARK 465 GLY A 40 REMARK 465 GLY A 41 REMARK 465 GLY A 42 REMARK 465 SER A 43 REMARK 465 SER A 44 REMARK 465 ALA A 45 REMARK 465 ALA A 46 REMARK 465 PRO A 47 REMARK 465 ALA A 48 REMARK 465 GLY A 49 REMARK 465 GLY 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 THR A 57 -140.70 -107.81 REMARK 500 1 LYS A 58 102.52 -50.93 REMARK 500 1 TRP A 65 143.66 -178.76 REMARK 500 2 THR A 57 -151.40 -98.05 REMARK 500 2 TRP A 65 148.18 -176.43 REMARK 500 3 THR A 57 -146.21 -99.22 REMARK 500 3 LYS A 58 108.01 -50.06 REMARK 500 3 TRP A 65 146.06 -174.72 REMARK 500 4 THR A 57 -148.94 -102.68 REMARK 500 4 TRP A 65 140.28 -179.31 REMARK 500 5 THR A 57 -149.99 -102.47 REMARK 500 5 LYS A 58 104.66 -48.25 REMARK 500 5 TRP A 65 139.55 -176.65 REMARK 500 6 THR A 57 -149.05 -101.99 REMARK 500 7 THR A 57 -147.42 -102.41 REMARK 500 7 LYS A 58 107.44 -51.93 REMARK 500 7 TRP A 65 140.06 -177.32 REMARK 500 8 THR A 57 -142.86 -96.38 REMARK 500 8 LYS A 58 103.28 -50.34 REMARK 500 8 TRP A 65 143.82 -176.14 REMARK 500 9 THR A 57 -150.97 -98.02 REMARK 500 9 TRP A 65 146.19 -176.14 REMARK 500 10 THR A 57 -147.94 -104.41 REMARK 500 10 LYS A 58 106.65 -48.11 REMARK 500 10 TRP A 65 146.87 -176.67 REMARK 500 11 THR A 57 -146.29 -97.51 REMARK 500 11 TRP A 65 139.49 176.70 REMARK 500 12 THR A 57 -153.43 -98.68 REMARK 500 12 TRP A 65 138.37 178.24 REMARK 500 13 THR A 57 -147.18 -99.20 REMARK 500 13 TRP A 65 139.39 -176.88 REMARK 500 14 THR A 57 -148.93 -99.91 REMARK 500 14 TRP A 65 139.15 -178.61 REMARK 500 15 THR A 57 -151.98 -100.61 REMARK 500 15 TRP A 65 143.01 -177.64 REMARK 500 16 THR A 57 -146.57 -98.10 REMARK 500 16 TRP A 65 147.63 -175.80 REMARK 500 17 THR A 57 -149.51 -96.19 REMARK 500 17 TRP A 65 140.08 -177.77 REMARK 500 18 THR A 57 -134.80 -108.84 REMARK 500 18 LYS A 58 102.65 -54.71 REMARK 500 19 THR A 57 -134.77 -105.66 REMARK 500 19 TRP A 65 139.53 -177.23 REMARK 500 20 THR A 57 -149.09 -98.12 REMARK 500 20 TRP A 65 138.94 -177.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36306 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF COLD SHOCK DOMAIN AND SSDNA COMPLEX DBREF 6LMR A 44 140 UNP P67809 YBOX1_HUMAN 44 140 DBREF 6LMR B 301 307 PDB 6LMR 6LMR 301 307 SEQADV 6LMR MET A 28 UNP P67809 INITIATING METHIONINE SEQADV 6LMR HIS A 29 UNP P67809 EXPRESSION TAG SEQADV 6LMR HIS A 30 UNP P67809 EXPRESSION TAG SEQADV 6LMR HIS A 31 UNP P67809 EXPRESSION TAG SEQADV 6LMR HIS A 32 UNP P67809 EXPRESSION TAG SEQADV 6LMR HIS A 33 UNP P67809 EXPRESSION TAG SEQADV 6LMR HIS A 34 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 35 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 36 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 37 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 38 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 39 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 40 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 41 UNP P67809 EXPRESSION TAG SEQADV 6LMR GLY A 42 UNP P67809 EXPRESSION TAG SEQADV 6LMR SER A 43 UNP P67809 EXPRESSION TAG SEQRES 1 A 113 MET HIS HIS HIS HIS HIS HIS GLY GLY GLY GLY GLY GLY SEQRES 2 A 113 GLY GLY SER SER ALA ALA PRO ALA GLY GLY ASP LYS LYS SEQRES 3 A 113 VAL ILE ALA THR LYS VAL LEU GLY THR VAL LYS TRP PHE SEQRES 4 A 113 ASN VAL ARG ASN GLY TYR GLY PHE ILE ASN ARG ASN ASP SEQRES 5 A 113 THR LYS GLU ASP VAL PHE VAL HIS GLN THR ALA ILE LYS SEQRES 6 A 113 LYS ASN ASN PRO ARG LYS TYR LEU ARG SER VAL GLY ASP SEQRES 7 A 113 GLY GLU THR VAL GLU PHE ASP VAL VAL GLU GLY GLU LYS SEQRES 8 A 113 GLY ALA GLU ALA ALA ASN VAL THR GLY PRO GLY GLY VAL SEQRES 9 A 113 PRO VAL GLN GLY SER LYS TYR ALA ALA SEQRES 1 B 7 DA DA DC DA DC DC DT 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 ALA A 120 THR A 126 1 O ALA A 122 N PHE A 85 SHEET 5 AA1 6 THR A 108 GLU A 115 -1 N GLU A 110 O THR A 126 SHEET 6 AA1 6 VAL A 54 ASN A 67 -1 N GLY A 61 O VAL A 109 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