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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN APOBEC3B VARIANT COMPLEXED WITH SSDNA
 
Authors :  K. Shi, S. Banerjee, K. Kurahashi, H. Aihara
Date :  16 Sep 16  (Deposition) - 28 Dec 16  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Deaminase, Dna Substrate Complex, 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-3B
    Chains: A
    EC Number: 3.5.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: APOBEC3B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: A3B,PHORBOLIN-1-RELATED PROTEIN,PHORBOLIN-2/3
 
Molecule 2 - DNA (5'-D(P*TP*TP*CP*AP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3IOD9Ligand/IonIODIDE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:253 , CYS A:284 , CYS A:289 , CL A:417binding site for residue ZN A 401
02AC2SOFTWAREHOH A:569binding site for residue IOD A 403
03AC3SOFTWAREASP A:194 , DA C:1binding site for residue IOD A 404
04AC4SOFTWAREARG A:211 , HIS A:212 , DT C:-2binding site for residue IOD A 405
05AC5SOFTWAREARG A:211 , HIS A:212 , DT C:-2 , DA C:1binding site for residue IOD A 407
06AC6SOFTWAREHOH A:527binding site for residue EDO A 410
07AC7SOFTWAREGLY A:251 , ARG A:252 , HIS A:253 , LEU A:256 , TRP A:287 , CYS A:289 , EDO A:412 , HOH A:502binding site for residue EDO A 411
08AC8SOFTWAREHIS A:253 , TRP A:287 , TYR A:313 , EDO A:411 , DC C:0 , DA C:1binding site for residue EDO A 412
09AC9SOFTWAREARG A:374 , LEU A:377 , HOH A:508binding site for residue EDO A 413
10AD1SOFTWAREARG A:190 , TYR A:191 , TYR A:218 , GLY A:236 , PHE A:237 , HOH A:550binding site for residue EDO A 414
11AD2SOFTWAREGLY A:205 , TRP A:281 , DT C:-1binding site for residue EDO A 415
12AD3SOFTWAREHIS A:365binding site for residue CL A 416
13AD4SOFTWAREHIS A:253 , PRO A:283 , CYS A:284 , CYS A:289 , ZN A:401 , DC C:0binding site for residue CL A 417
14AD5SOFTWAREASP A:194 , DA C:1binding site for residue IOD C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TD5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TD5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TD5)

(-) Exons   (0, 0)

(no "Exon" information available for 5TD5)

(-) Sequences/Alignments

Asymmetric/Biological 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:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh........eeeeeeeee....eee.hhhheeee.....hhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5td5 A 190 RYLMDPDTFTSNFNNGIGRHKTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQL 379
                                   199     ||212       222       232       250       260       270       280       290       300       310       320       330       340       350       360       370         
                                         205|                             241|                                                                                                                                 
                                          209                              250                                                                                                                                 


Chain C from PDB  Type:DNA  Length:5
                                     
                 5td5 C  -2 TTCAT   2
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5TD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TD5)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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        ABC3B_HUMAN | Q9UH17: 2nbq 5cqd 5cqh 5cqi 5cqk 5tkm

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