PDB Short entry for 2D9L HEADER GENE REGULATION 11-DEC-05 2D9L TITLE SOLUTION STRUCTURE OF THE ARFGAP DOMAIN OF HUMAN RIP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPORIN-LIKE PROTEIN RIP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ARFGAP DOMAIN; COMPND 5 SYNONYM: HIV-1 REV-BINDING PROTEIN, REV INTERACTING PROTEIN, REV/REX COMPND 6 ACTIVATION DOMAIN-BINDING PROTEIN; COMPND 7 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: HRB; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050302-26; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS RIP, HIV-1, REV, ARFGAP DOMAIN, ZINC FINGER, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SUETAKE,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2D9L 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2D9L 1 VERSN REVDAT 1 11-DEC-06 2D9L 0 JRNL AUTH T.SUETAKE,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE ARFGAP DOMAIN OF HUMAN RIP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D9L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025156. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.39MM 13C, 15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL; 100MM NACL; 1MM REMARK 210 D-DTT; 0.02% NAN3; 0.05MM ZNCL2; REMARK 210 1MM IDA; 90% H2O; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.932, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATION, TARGET REMARK 210 FUNCTION 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: 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 SER A 5 126.74 -174.79 REMARK 500 1 LEU A 17 153.64 -42.09 REMARK 500 1 CYS A 23 -179.86 -62.32 REMARK 500 1 ASP A 25 -70.95 -109.10 REMARK 500 1 HIS A 57 -177.83 -60.15 REMARK 500 1 HIS A 78 -75.56 -106.16 REMARK 500 1 PHE A 91 133.34 -39.40 REMARK 500 1 ASP A 93 -37.47 -35.17 REMARK 500 1 PRO A 99 -167.11 -69.77 REMARK 500 1 TRP A 120 40.18 -84.90 REMARK 500 1 GLU A 125 -38.39 -39.88 REMARK 500 2 LEU A 17 151.28 -46.86 REMARK 500 2 ASP A 27 29.87 47.51 REMARK 500 2 HIS A 57 -175.50 -61.27 REMARK 500 2 SER A 61 151.42 -44.71 REMARK 500 2 HIS A 78 -75.33 -109.35 REMARK 500 2 PHE A 91 138.50 -37.12 REMARK 500 2 PRO A 99 -177.50 -69.80 REMARK 500 2 PHE A 101 47.36 -107.86 REMARK 500 2 ARG A 102 -43.72 -133.70 REMARK 500 2 TRP A 120 51.38 -90.44 REMARK 500 3 LEU A 17 153.68 -45.33 REMARK 500 3 CYS A 23 172.86 -56.99 REMARK 500 3 ASP A 25 -64.85 -132.37 REMARK 500 3 ASP A 27 51.41 34.95 REMARK 500 3 ARG A 29 145.12 -38.66 REMARK 500 3 LEU A 53 171.20 -57.05 REMARK 500 3 HIS A 57 -178.68 -62.16 REMARK 500 3 HIS A 78 -75.38 -117.09 REMARK 500 3 PHE A 91 142.82 -38.58 REMARK 500 3 SER A 95 -71.97 -85.25 REMARK 500 3 PRO A 99 -174.52 -69.80 REMARK 500 3 GLU A 125 -35.01 -37.74 REMARK 500 4 LEU A 17 151.93 -47.62 REMARK 500 4 CYS A 23 173.33 -56.67 REMARK 500 4 ASP A 25 -68.61 -109.11 REMARK 500 4 SER A 47 -31.47 -37.75 REMARK 500 4 HIS A 57 -175.08 -61.69 REMARK 500 4 SER A 61 154.20 -48.64 REMARK 500 4 HIS A 78 -75.14 -99.99 REMARK 500 4 PRO A 99 -175.97 -69.73 REMARK 500 4 TRP A 120 49.75 -86.83 REMARK 500 5 SER A 5 42.37 -93.91 REMARK 500 5 ARG A 21 -33.44 -36.30 REMARK 500 5 CYS A 23 -179.77 -51.86 REMARK 500 5 ARG A 29 105.37 -45.92 REMARK 500 5 GLN A 69 -39.29 -34.22 REMARK 500 5 HIS A 78 -75.45 -119.00 REMARK 500 5 SER A 95 -70.41 -38.25 REMARK 500 5 ARG A 119 -70.25 -58.46 REMARK 500 REMARK 500 THIS ENTRY HAS 235 RAMACHANDRAN OUTLIERS. 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 105.0 REMARK 620 3 CYS A 43 SG 104.7 105.7 REMARK 620 4 CYS A 46 SG 113.3 116.9 110.2 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 ZN A 401 DBREF 2D9L A 8 128 UNP P52594 NUPL_HUMAN 14 134 SEQADV 2D9L GLY A 1 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 2 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 3 UNP P52594 CLONING ARTIFACT SEQADV 2D9L GLY A 4 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 5 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 6 UNP P52594 CLONING ARTIFACT SEQADV 2D9L GLY A 7 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 129 UNP P52594 CLONING ARTIFACT SEQADV 2D9L GLY A 130 UNP P52594 CLONING ARTIFACT SEQADV 2D9L PRO A 131 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 132 UNP P52594 CLONING ARTIFACT SEQADV 2D9L SER A 133 UNP P52594 CLONING ARTIFACT SEQADV 2D9L GLY A 134 UNP P52594 CLONING ARTIFACT SEQRES 1 A 134 GLY SER SER GLY SER SER GLY LEU LYS MET LEU ARG ASP SEQRES 2 A 134 MET THR GLY LEU PRO HIS ASN ARG LYS CYS PHE ASP CYS SEQRES 3 A 134 ASP GLN ARG GLY PRO THR TYR VAL ASN MET THR VAL GLY SEQRES 4 A 134 SER PHE VAL CYS THR SER CYS SER GLY SER LEU ARG GLY SEQRES 5 A 134 LEU ASN PRO PRO HIS ARG VAL LYS SER ILE SER MET THR SEQRES 6 A 134 THR PHE THR GLN GLN GLU ILE GLU PHE LEU GLN LYS HIS SEQRES 7 A 134 GLY ASN GLU VAL CYS LYS GLN ILE TRP LEU GLY LEU PHE SEQRES 8 A 134 ASP ASP ARG SER SER ALA ILE PRO ASP PHE ARG ASP PRO SEQRES 9 A 134 GLN LYS VAL LYS GLU PHE LEU GLN GLU LYS TYR GLU LYS SEQRES 10 A 134 LYS ARG TRP TYR VAL PRO PRO GLU GLN ALA LYS SER GLY SEQRES 11 A 134 PRO SER SER GLY HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 GLY A 7 THR A 15 1 9 HELIX 2 2 CYS A 43 LEU A 53 1 11 HELIX 3 3 THR A 68 LYS A 77 1 10 HELIX 4 4 HIS A 78 LEU A 88 1 11 HELIX 5 5 ASP A 103 TYR A 115 1 13 HELIX 6 6 PRO A 123 LYS A 128 1 6 SHEET 1 A 2 TYR A 33 ASN A 35 0 SHEET 2 A 2 VAL A 59 SER A 61 -1 O LYS A 60 N VAL A 34 LINK SG CYS A 23 ZN ZN A 401 1555 1555 2.35 LINK SG CYS A 26 ZN ZN A 401 1555 1555 2.26 LINK SG CYS A 43 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 46 ZN ZN A 401 1555 1555 2.26 CISPEP 1 ASN A 54 PRO A 55 1 -0.12 CISPEP 2 ASN A 54 PRO A 55 2 -0.06 CISPEP 3 ASN A 54 PRO A 55 3 0.00 CISPEP 4 ASN A 54 PRO A 55 4 -0.08 CISPEP 5 ASN A 54 PRO A 55 5 -0.08 CISPEP 6 ASN A 54 PRO A 55 6 -0.03 CISPEP 7 ASN A 54 PRO A 55 7 -0.11 CISPEP 8 ASN A 54 PRO A 55 8 -0.09 CISPEP 9 ASN A 54 PRO A 55 9 -0.11 CISPEP 10 ASN A 54 PRO A 55 10 -0.16 CISPEP 11 ASN A 54 PRO A 55 11 -0.06 CISPEP 12 ASN A 54 PRO A 55 12 -0.16 CISPEP 13 ASN A 54 PRO A 55 13 -0.08 CISPEP 14 ASN A 54 PRO A 55 14 -0.07 CISPEP 15 ASN A 54 PRO A 55 15 0.00 CISPEP 16 ASN A 54 PRO A 55 16 0.00 CISPEP 17 ASN A 54 PRO A 55 17 -0.01 CISPEP 18 ASN A 54 PRO A 55 18 -0.06 CISPEP 19 ASN A 54 PRO A 55 19 -0.09 CISPEP 20 ASN A 54 PRO A 55 20 -0.07 SITE 1 AC1 4 CYS A 23 CYS A 26 CYS A 43 CYS A 46 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