HEADER HYDROLASE 20-DEC-07 2JYW TITLE SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF APOBEC3G COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3G; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: APOBEC-RELATED CYTIDINE DEAMINASE, ARCD, APOBEC-RELATED COMPND 6 PROTEIN, ARP-9, CEM15, CEM-15; COMPND 7 EC: 3.5.4.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APOBEC3G; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P2_A3G198-384 KEYWDS PROTEIN, ZINC, ALTERNATIVE SPLICING, ANTIVIRAL DEFENSE, CYTOPLASM, KEYWDS 2 HOST-VIRUS INTERACTION, HYDROLASE, METAL-BINDING, NUCLEUS, KEYWDS 3 POLYMORPHISM, UBL CONJUGATION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.CHEN,E.HARJES,P.J.GROSS,A.FAHMY,Y.LU,K.SHINDO,R.S.HARRIS,H.MATSUO REVDAT 6 29-MAY-24 2JYW 1 REMARK REVDAT 5 20-OCT-21 2JYW 1 REMARK SEQADV REVDAT 4 24-FEB-09 2JYW 1 VERSN REVDAT 3 27-MAY-08 2JYW 1 SSBOND REVDAT 2 18-MAR-08 2JYW 1 JRNL REVDAT 1 26-FEB-08 2JYW 0 JRNL AUTH K.M.CHEN,E.HARJES,P.J.GROSS,A.FAHMY,Y.LU,K.SHINDO, JRNL AUTH 2 R.S.HARRIS,H.MATSUO JRNL TITL STRUCTURE OF THE DNA DEAMINASE DOMAIN OF THE HIV-1 JRNL TITL 2 RESTRICTION FACTOR APOBEC3G. JRNL REF NATURE V. 452 116 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18288108 JRNL DOI 10.1038/NATURE06638 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, A.T. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JYW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000100463. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 300 MM [U-100% 15N] APOBEC3G, REMARK 210 95% H2O/5% D2O; 300 MM [U-100% REMARK 210 13C; U-100% 15N; 80% 2H] REMARK 210 APOBEC3G, 95% H2O/5% D2O; 300 MM REMARK 210 [U-100% 15N, 80%2H] APOBEC3G, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D H(CCO)NH; 3D HNCACO; REMARK 210 3D HN(COCA)CB; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8.3, NMRDRAW 2.5, REMARK 210 ATNOS/CANDID 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY, RAMACHANDRAN REMARK 210 PARAMETERS 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -7 REMARK 465 PRO A -6 REMARK 465 LEU A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 PRO A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 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 ASN A 10 -167.85 -69.81 REMARK 500 1 TRP A 14 54.46 -172.12 REMARK 500 1 VAL A 15 -80.61 -172.55 REMARK 500 1 ARG A 18 -160.42 -63.67 REMARK 500 1 HIS A 19 -172.63 57.06 REMARK 500 1 GLU A 20 83.16 -58.37 REMARK 500 1 ASN A 47 -172.54 -178.28 REMARK 500 1 ALA A 49 108.56 66.10 REMARK 500 1 HIS A 53 108.88 61.95 REMARK 500 1 LEU A 56 -66.87 -128.04 REMARK 500 1 HIS A 60 76.70 -103.27 REMARK 500 1 ALA A 61 -66.14 66.90 REMARK 500 1 LEU A 74 167.87 -49.72 REMARK 500 1 ASP A 75 -70.63 -67.93 REMARK 500 1 LEU A 76 -44.72 179.87 REMARK 500 1 SER A 89 -75.76 -64.48 REMARK 500 1 PRO A 90 -162.29 -110.86 REMARK 500 1 LYS A 100 -71.09 -54.93 REMARK 500 1 PHE A 101 -34.13 -37.64 REMARK 500 1 HIS A 107 44.73 -178.49 REMARK 500 1 ARG A 116 159.83 176.04 REMARK 500 1 GLN A 121 -38.17 -177.69 REMARK 500 1 ALA A 124 -42.19 -174.14 REMARK 500 1 LEU A 128 -70.63 -62.82 REMARK 500 1 ALA A 136 175.16 178.06 REMARK 500 1 TYR A 143 -41.26 -27.68 REMARK 500 1 GLN A 157 88.36 59.31 REMARK 500 1 ALA A 159 156.96 -45.58 REMARK 500 1 PRO A 160 60.19 -66.81 REMARK 500 1 GLN A 185 91.15 -57.69 REMARK 500 2 PRO A 2 107.48 -55.21 REMARK 500 2 ASN A 11 -29.11 -39.58 REMARK 500 2 PRO A 13 101.75 -39.50 REMARK 500 2 TRP A 14 -167.32 -68.35 REMARK 500 2 ARG A 16 26.92 -149.73 REMARK 500 2 ARG A 18 -172.95 -52.51 REMARK 500 2 HIS A 19 -12.67 79.59 REMARK 500 2 GLU A 20 41.50 175.25 REMARK 500 2 TYR A 22 88.63 -60.67 REMARK 500 2 ASN A 39 89.51 62.89 REMARK 500 2 ASN A 47 -169.55 -167.87 REMARK 500 2 ALA A 49 166.33 57.49 REMARK 500 2 PHE A 55 138.33 64.02 REMARK 500 2 HIS A 60 79.69 -102.11 REMARK 500 2 ALA A 61 -65.27 66.70 REMARK 500 2 LEU A 74 -163.56 -75.89 REMARK 500 2 ASP A 75 -82.83 -69.01 REMARK 500 2 LEU A 76 -33.11 174.59 REMARK 500 2 SER A 89 -73.75 -63.67 REMARK 500 2 PRO A 90 -163.00 -109.94 REMARK 500 REMARK 500 THIS ENTRY HAS 317 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 188 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 60 ND1 REMARK 620 2 CYS A 91 SG 139.5 REMARK 620 3 CYS A 94 SG 78.7 61.9 REMARK 620 N 1 2 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 188 DBREF 2JYW A 1 187 UNP Q9HC16 ABC3G_HUMAN 198 384 SEQADV 2JYW GLY A -7 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW PRO A -6 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW LEU A -5 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW GLY A -4 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW SER A -3 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW PRO A -2 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW GLU A -1 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW PHE A 0 UNP Q9HC16 EXPRESSION TAG SEQADV 2JYW LYS A 37 UNP Q9HC16 LEU 234 ENGINEERED MUTATION SEQADV 2JYW ALA A 46 UNP Q9HC16 CYS 243 ENGINEERED MUTATION SEQADV 2JYW LYS A 113 UNP Q9HC16 PHE 310 ENGINEERED MUTATION SEQADV 2JYW ALA A 124 UNP Q9HC16 CYS 321 ENGINEERED MUTATION SEQADV 2JYW ALA A 159 UNP Q9HC16 CYS 356 ENGINEERED MUTATION SEQRES 1 A 195 GLY PRO LEU GLY SER PRO GLU PHE ASP PRO PRO THR PHE SEQRES 2 A 195 THR PHE ASN PHE ASN ASN GLU PRO TRP VAL ARG GLY ARG SEQRES 3 A 195 HIS GLU THR TYR LEU CYS TYR GLU VAL GLU ARG MET HIS SEQRES 4 A 195 ASN ASP THR TRP VAL LYS LEU ASN GLN ARG ARG GLY PHE SEQRES 5 A 195 LEU ALA ASN GLN ALA PRO HIS LYS HIS GLY PHE LEU GLU SEQRES 6 A 195 GLY ARG HIS ALA GLU LEU CYS PHE LEU ASP VAL ILE PRO SEQRES 7 A 195 PHE TRP LYS LEU ASP LEU ASP GLN ASP TYR ARG VAL THR SEQRES 8 A 195 CYS PHE THR SER TRP SER PRO CYS PHE SER CYS ALA GLN SEQRES 9 A 195 GLU MET ALA LYS PHE ILE SER LYS ASN LYS HIS VAL SER SEQRES 10 A 195 LEU CYS ILE LYS THR ALA ARG ILE TYR ASP ASP GLN GLY SEQRES 11 A 195 ARG ALA GLN GLU GLY LEU ARG THR LEU ALA GLU ALA GLY SEQRES 12 A 195 ALA LYS ILE SER ILE MET THR TYR SER GLU PHE LYS HIS SEQRES 13 A 195 CYS TRP ASP THR PHE VAL ASP HIS GLN GLY ALA PRO PHE SEQRES 14 A 195 GLN PRO TRP ASP GLY LEU ASP GLU HIS SER GLN ASP LEU SEQRES 15 A 195 SER GLY ARG LEU ARG ALA ILE LEU GLN ASN GLN GLU ASN HET ZN A 188 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ALA A 61 LYS A 73 1 13 HELIX 2 2 CYS A 91 LYS A 104 1 14 HELIX 3 3 ALA A 124 GLY A 135 1 12 HELIX 4 4 THR A 142 VAL A 154 1 13 HELIX 5 5 ASP A 165 ASN A 184 1 20 SHEET 1 A 5 THR A 34 VAL A 36 0 SHEET 2 A 5 CYS A 24 HIS A 31 -1 N HIS A 31 O THR A 34 SHEET 3 A 5 ASP A 79 PHE A 85 -1 O PHE A 85 N CYS A 24 SHEET 4 A 5 VAL A 108 THR A 114 1 O LYS A 113 N CYS A 84 SHEET 5 A 5 LYS A 137 ILE A 140 1 O SER A 139 N THR A 114 LINK ND1 HIS A 60 ZN ZN A 188 1555 1555 2.01 LINK SG CYS A 91 ZN ZN A 188 1555 1555 2.31 LINK SG CYS A 94 ZN ZN A 188 1555 1555 2.29 SITE 1 AC1 4 ARG A 16 GLY A 17 ARG A 18 GLU A 62 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