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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN APOBEC3A COMPLEXED WITH SSDNA
 
Authors :  K. Shi, S. Banerjee, K. Kurahashi, H. Aihara
Date :  09 Aug 16  (Deposition) - 28 Dec 16  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Apobec3A, Cytidine Deaminase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shi, M. A. Carpenter, S. Banerjee, N. M. Shaban, K. Kurahashi, D. J. Salamango, J. L. Mccann, G. J. Starrett, J. V. Duffy, O. Demir, R. E. Amaro, D. A. Harki, R. S. Harris, H. Aihara
Structural Basis For Targeted Dna Cytosine Deamination And Mutagenesis By Apobec3A And Apobec3B.
Nat. Struct. Mol. Biol. V. 24 131 2017
PubMed-ID: 27991903  |  Reference-DOI: 10.1038/NSMB.3344

(-) Compounds

Molecule 1 - DNA DC->DU-EDITING ENZYME APOBEC-3A
    Chains: A, B, C, D
    EC Number: 3.5.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: APOBEC3A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: A3A,PHORBOLIN-1
 
Molecule 2 - DNA 15-MER
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:70 , CYS A:101 , CYS A:106binding site for residue ZN A 201
2AC2SOFTWAREHIS B:70 , CYS B:101 , CYS B:106binding site for residue ZN B 201
3AC3SOFTWARETYR B:35 , HIS B:51 , ARG B:52binding site for residue GOL B 202
4AC4SOFTWAREARG B:123 , GLU B:157 , HIS B:160binding site for residue GOL B 203
5AC5SOFTWAREHIS C:70 , CYS C:101 , CYS C:106binding site for residue ZN C 201
6AC6SOFTWAREHIS D:70 , CYS D:101 , CYS D:106binding site for residue ZN D 201
7AC7SOFTWAREDA F:-2binding site for residue GOL F 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5SWW)

(-) 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:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.........eeeeeeee.....eeeeeeeee.............hhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sww A  10 RHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDSVKMDQHRGFLHNQAKNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQ 195
                                    19        29        39 ||     52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
                                                          41|                                                                                                                                                      
                                                           45                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.........eeeeeeeee.....eeeeeeee.............hhhhhhhhhhhhhh.....eeeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sww B  10 RHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDSVKMDQHRGFLHNQAKNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQ 195
                                    19        29        39 ||     52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
                                                          41|                                                                                                                                                      
                                                           45                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.........eeeeeeeee.....eeeeeee.............hhhhhhhhhhhhhh.....eeeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sww C   8 GPRHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGMDQHRGFLHNQAKNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQN 196
                                    17        27        37     || 51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
                                                              43|                                                                                                                                                    
                                                               48                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.........eeeeeeee.......eeeeeee.............hhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sww D   7 SGPRHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGKMDQHRGFLHNQAKNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQN 196
                                    16        26        36      ||49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       
                                                               43|                                                                                                                                                     
                                                                47                                                                                                                                                     


Chain E from PDB  Type:DNA  Length:6
                                      
                 5sww E  -2 ATCGGG   3


Chain F from PDB  Type:DNA  Length:6
                                      
                 5sww F  -2 ATCGGG   3


Chain G from PDB  Type:DNA  Length:6
                                      
                 5sww G  -2 ATCGGG   3


Chain H from PDB  Type:DNA  Length:6
                                      
                 5sww H  -2 ATCGGG   3
   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 5SWW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

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        ABC3A_HUMAN | P31941: 2m65 4xxo 5keg

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