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(-) Description

Title :  CRYSTAL STRUCTURE OF A PRIMATE APOBEC3G N-DOMAIN, IN COMPLEX WITH SSDNA
 
Authors :  X. Xiao, S. -X. Li, H. Yang, X. S. Chen
Date :  27 May 16  (Deposition) - 10 Aug 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C,D,E,F,H,I,J
Biol. Unit 1:  C,D,I  (1x)
Biol. Unit 2:  E,F,J  (1x)
Biol. Unit 3:  A,B,H  (1x)
Keywords :  Apobec3G, Vif, Hiv, Apobec, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xiao, S. X. Li, H. Yang, X. S. Chen
Crystal Structures Of Apobec3G N-Domain Alone And Its Complex With Dna.
Nat Commun V. 7 12193 2016
PubMed-ID: 27480941  |  Reference-DOI: 10.1038/NCOMMS12193

(-) Compounds

Molecule 1 - APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE- LIKE 3G,APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE-LIKE 3G
    Chains: D, C, F, E, B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: UNP RESIDUES 1-195 (139CQKRDGPH146 REPLACED BY AEAG)
    Gene: APOBEC3G
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
 
Molecule 2 - DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    Chains: I, J, H
    Engineered: YES
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFHIJ
Biological Unit 1 (1x):   CD   I 
Biological Unit 2 (1x):     EF  J
Biological Unit 3 (1x): AB    H  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS D:65 , CYS D:97 , CYS D:100 , HOH D:517binding site for residue ZN D 401
2AC2SOFTWAREHIS C:65 , CYS C:97 , CYS C:100 , HOH I:103binding site for residue ZN C 401
3AC3SOFTWAREHIS F:65 , CYS F:97 , CYS F:100 , HOH F:513binding site for residue ZN F 401
4AC4SOFTWAREHIS E:65 , CYS E:97 , CYS E:100 , HOH E:507binding site for residue ZN E 401
5AC5SOFTWAREHIS B:65 , CYS B:97 , CYS B:100 , HOH B:505binding site for residue ZN B 401
6AC6SOFTWAREHIS A:65 , CYS A:97 , CYS A:100 , HOH A:510binding site for residue ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K83)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K83)

(-) Exons   (0, 0)

(no "Exon" information available for 5K83)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...hhhhhhh............eeeeeeeeee........eeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k83 A   1 MKPQIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194 
                                                                                                                                                                   138|                                                    
                                                                                                                                                                    143                                                    


Chain B from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh..........eeeeeeeeee........eeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k83 B   7 NMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    16        26        36        46        56        66        76        86        96       106       116       126       136 ||    150       160       170       180       190     
                                                                                                                                                             138|                                                    
                                                                                                                                                              143                                                    


Chain C from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...hhhhhhh............eeeeeeeeee........eeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k83 C   1 MKPQIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194 
                                                                                                                                                                   138|                                                    
                                                                                                                                                                    143                                                    


Chain D from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh..........eeeeeeeeee........eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k83 D   7 NMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    16        26        36        46        56        66        76        86        96       106       116       126       136 ||    150       160       170       180       190     
                                                                                                                                                             138|                                                    
                                                                                                                                                              143                                                    


Chain E from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...hhhhhhh............eeeeeeeeee......eeeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k83 E   1 MKPQIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194 
                                                                                                                                                                   138|                                                    
                                                                                                                                                                    143                                                    


Chain F from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..........eeeeeeeeee........eeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k83 F   8 MVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    17        27        37        47        57        67        77        87        97       107       117       127       137||     151       161       171       181       191    
                                                                                                                                                            138|                                                    
                                                                                                                                                             143                                                    


Chain H from PDB  Type:DNA  Length:3
                                   
                 5k83 H  10 TTT  12


Chain I from PDB  Type:DNA  Length:3
                                   
                 5k83 I  10 TTT  12


Chain J from PDB  Type:DNA  Length:3
                                   
                 5k83 J  10 TTT  12
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5K83)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K83)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K83)

(-) Gene Ontology  (4, 4)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        M1GSK9_MACMU | M1GSK9: 5k81 5k82

(-) Related Entries Specified in the PDB File

5k81 5k82