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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN APOBEC3C HAVING HIV-1 VIF-BINDING INTERFACE
 
Authors :  S. Kitamura, A. Suzuki, N. Watanabe, Y. Iwatani
Date :  09 Dec 11  (Deposition) - 03 Oct 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Apobec3C, Sivagm, Metal-Binding, Single Domain, Z2, Antiviral Defense, Host-Virus Interaction, Hydrolase, Hiv, Hiv-1 Vif, Bet (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kitamura, H. Ode, M. Nakashima, M. Imahashi, Y. Naganawa, S. Ibe, Y. Yokomaku, N. Watanabe, A. Suzuki, W. Sugiura, Y. Iwatani
Crystal Structure Of The Human Apobec3C Having Hiv-1 Vif-Binding Interface
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE DNA DC->DU-EDITING ENZYME APOBEC-3C
    ChainsA, B
    EC Number3.5.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET41A(+)
    Expression System StrainROSETTA2(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAPOBEC3C, APOBEC1L, PBI
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPOBEC1-LIKE, PHORBOLIN I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , CYS A:97 , CYS A:100BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS B:66 , GLU B:68 , CYS B:97 , CYS B:100BINDING SITE FOR RESIDUE ZN B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VM8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:48 -Ser A:49
2Ser A:61 -Glu A:62

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VM8)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.ABC3C_HUMAN29-138
 
  2A:29-138
B:29-138
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.ABC3C_HUMAN66-104
 
  2A:66-104
B:66-104
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.ABC3C_HUMAN29-138
 
  1A:29-138
-
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.ABC3C_HUMAN66-104
 
  1A:66-104
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.ABC3C_HUMAN29-138
 
  1-
B:29-138
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.ABC3C_HUMAN66-104
 
  1-
B:66-104

(-) Exons   (0, 0)

(no "Exon" information available for 3VM8)

(-) 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:187
 aligned with ABC3C_HUMAN | Q9NRW3 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
          ABC3C_HUMAN     4 QIRNPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILSPNTKYQVTWYTSWSPCPDCAGEVAEFLARHSNVNLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESLQ 190
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..........eeeeeeeeeee.......eeeeeeeee.......hhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------CYT_DCMP_DEAMINASES_2  PDB: A:29-138 UniProt: 29-138                                                          ---------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:66-104   -------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vm8 A   4 QIRNPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILSPNTKYQVTWYTSWSPCPDCAGEVAEFLARHSNVNLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESLQ 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       

Chain B from PDB  Type:PROTEIN  Length:187
 aligned with ABC3C_HUMAN | Q9NRW3 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
          ABC3C_HUMAN     4 QIRNPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILSPNTKYQVTWYTSWSPCPDCAGEVAEFLARHSNVNLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESLQ 190
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh............eeeeeeee......eeeeeee..........hhhhhhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------CYT_DCMP_DEAMINASES_2  PDB: B:29-138 UniProt: 29-138                                                          ---------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:66-104   -------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vm8 B   4 QIRNPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILSPNTKYQVTWYTSWSPCPDCAGEVAEFLARHSNVNLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESLQ 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       

   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 3VM8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VM8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VM8)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ABC3C_HUMAN | Q9NRW3)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016814    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amidine, a compound of the form R-C(=NH)-NH2.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0080111    DNA demethylation    The removal of a methyl group from one or more nucleotides within an DNA molecule.
    GO:0009972    cytidine deamination    The removal of amino group in the presence of water.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0010529    negative regulation of transposition    Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        ABC3C_HUMAN | Q9NRW33vow

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