HEADER DNA BINDING PROTEIN 02-DEC-20 7DM4 TITLE SOLUTION STRUCTURE OF ARID4B TUDOR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 4B; COMPND 3 CHAIN: A; COMPND 4 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: ARID4B, BRCAA1, RBBP1L1, RBP1L1, SAP180; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARID4B, INTERDIGITATED, TUDOR, DISORDER REGION, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.REN,H.YAO,W.HU,S.PERRETT,Y.FENG,W.GONG REVDAT 5 15-MAY-24 7DM4 1 REMARK REVDAT 4 14-JUN-23 7DM4 1 REMARK REVDAT 3 21-JUL-21 7DM4 1 JRNL REVDAT 2 17-MAR-21 7DM4 1 JRNL REVDAT 1 10-MAR-21 7DM4 0 JRNL AUTH J.REN,H.YAO,W.HU,S.PERRETT,W.GONG,Y.FENG JRNL TITL STRUCTURAL BASIS FOR THE DNA-BINDING ACTIVITY OF HUMAN JRNL TITL 2 ARID4B TUDOR DOMAIN. JRNL REF J.BIOL.CHEM. V. 296 00506 2021 JRNL REFN ESSN 1083-351X JRNL PMID 33675746 JRNL DOI 10.1016/J.JBC.2021.100506 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019672. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 302 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.14 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-13C; U-15N] ARID4B REMARK 210 TUDOR DOMAIN, 2 MM DTT, 2 MM REMARK 210 EDTA, 100 MM SODIUM CHLORIDE, 20 REMARK 210 MM SODIUM PHOSPHATE, 90% H2O/10% REMARK 210 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 HNCACB; 3D REMARK 210 HN(CA)CO; 3D CBCA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D HBHA(CO) REMARK 210 NH; 3D C(CO)NH; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRVIEWJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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 2 -61.16 -97.18 REMARK 500 1 LEU A 4 72.53 59.39 REMARK 500 1 ALA A 86 79.59 -107.23 REMARK 500 1 GLU A 111 61.85 61.95 REMARK 500 1 ARG A 112 113.19 -162.71 REMARK 500 1 HIS A 113 15.79 -150.01 REMARK 500 1 PHE A 114 123.63 70.77 REMARK 500 1 VAL A 135 86.90 66.88 REMARK 500 1 ARG A 145 -61.19 70.00 REMARK 500 1 PRO A 150 84.03 -68.98 REMARK 500 2 LEU A 4 121.96 -177.78 REMARK 500 2 TYR A 9 134.57 59.44 REMARK 500 2 ARG A 21 -66.61 69.38 REMARK 500 2 ARG A 34 108.14 -50.71 REMARK 500 2 ALA A 86 28.56 -153.21 REMARK 500 2 LYS A 109 115.90 -36.62 REMARK 500 2 ARG A 112 17.74 -141.80 REMARK 500 2 LEU A 120 -85.10 61.95 REMARK 500 2 ASP A 121 71.69 42.52 REMARK 500 2 ILE A 136 16.70 51.07 REMARK 500 2 LYS A 139 -47.33 -174.15 REMARK 500 2 ASN A 141 -35.71 -131.72 REMARK 500 2 ARG A 142 -165.95 64.34 REMARK 500 2 ARG A 145 -30.58 72.81 REMARK 500 2 SER A 146 -26.27 74.87 REMARK 500 3 LEU A 4 178.92 67.72 REMARK 500 3 ASP A 5 69.94 -165.89 REMARK 500 3 ARG A 21 -72.03 69.49 REMARK 500 3 LYS A 109 -159.31 -136.42 REMARK 500 3 ARG A 112 111.94 -160.70 REMARK 500 3 PHE A 114 164.49 71.29 REMARK 500 3 SER A 117 87.31 65.22 REMARK 500 3 LEU A 123 82.94 62.45 REMARK 500 3 THR A 126 97.98 64.14 REMARK 500 3 PHE A 131 25.56 -162.65 REMARK 500 3 VAL A 135 101.18 65.75 REMARK 500 3 LYS A 138 88.76 63.31 REMARK 500 3 ARG A 142 -50.50 -126.51 REMARK 500 3 ASN A 147 74.63 -69.51 REMARK 500 3 HIS A 148 -32.87 -150.21 REMARK 500 4 LEU A 4 35.77 -90.38 REMARK 500 4 ALA A 86 74.38 -107.29 REMARK 500 4 GLU A 111 132.87 70.51 REMARK 500 4 ARG A 112 97.87 68.13 REMARK 500 4 HIS A 113 82.02 87.29 REMARK 500 4 PHE A 114 -153.19 -92.38 REMARK 500 4 GLU A 116 -63.70 68.78 REMARK 500 4 LEU A 120 96.63 62.40 REMARK 500 4 PRO A 128 89.43 -69.54 REMARK 500 4 HIS A 130 -30.16 164.77 REMARK 500 REMARK 500 THIS ENTRY HAS 205 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 43 0.09 SIDE CHAIN REMARK 500 4 ARG A 43 0.11 SIDE CHAIN REMARK 500 8 ARG A 43 0.09 SIDE CHAIN REMARK 500 14 ARG A 112 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50612 RELATED DB: BMRB DBREF 7DM4 A 1 151 UNP Q4LE39 ARI4B_HUMAN 1 151 SEQRES 1 A 151 MET LYS ALA LEU ASP GLU PRO PRO TYR LEU THR VAL GLY SEQRES 2 A 151 THR ASP VAL SER ALA LYS TYR ARG GLY ALA PHE CYS GLU SEQRES 3 A 151 ALA LYS ILE LYS THR ALA LYS ARG LEU VAL LYS VAL LYS SEQRES 4 A 151 VAL THR PHE ARG HIS ASP SER SER THR VAL GLU VAL GLN SEQRES 5 A 151 ASP ASP HIS ILE LYS GLY PRO LEU LYS VAL GLY ALA ILE SEQRES 6 A 151 VAL GLU VAL LYS ASN LEU ASP GLY ALA TYR GLN GLU ALA SEQRES 7 A 151 VAL ILE ASN LYS LEU THR ASP ALA SER TRP TYR THR VAL SEQRES 8 A 151 VAL PHE ASP ASP GLY ASP GLU LYS THR LEU ARG ARG SER SEQRES 9 A 151 SER LEU CYS LEU LYS GLY GLU ARG HIS PHE ALA GLU SER SEQRES 10 A 151 GLU THR LEU ASP GLN LEU PRO LEU THR ASN PRO GLU HIS SEQRES 11 A 151 PHE GLY THR PRO VAL ILE GLY LYS LYS THR ASN ARG GLY SEQRES 12 A 151 ARG ARG SER ASN HIS ILE PRO GLU SHEET 1 AA1 4 THR A 48 GLN A 52 0 SHEET 2 AA1 4 ALA A 23 PHE A 42 -1 N VAL A 40 O VAL A 49 SHEET 3 AA1 4 TYR A 75 VAL A 92 -1 O ASN A 81 N LYS A 39 SHEET 4 AA1 4 GLU A 98 ARG A 102 -1 O LYS A 99 N VAL A 91 SHEET 1 AA2 6 ILE A 56 LYS A 57 0 SHEET 2 AA2 6 ILE A 65 LYS A 69 -1 O GLU A 67 N LYS A 57 SHEET 3 AA2 6 TYR A 75 VAL A 92 -1 O ALA A 78 N VAL A 66 SHEET 4 AA2 6 ALA A 23 PHE A 42 -1 N LYS A 39 O ASN A 81 SHEET 5 AA2 6 ASP A 15 TYR A 20 -1 N VAL A 16 O ALA A 27 SHEET 6 AA2 6 LEU A 106 LEU A 108 -1 O CYS A 107 N SER A 17 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