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(-) Description

Title :  EVOLUTIONARY BASIS OF HIV RESTRICTION BY THE ANTIRETROVIRAL TRIMCYP
 
Authors :  A. J. Price, L. C. James
Date :  05 Mar 10  (Deposition) - 15 Sep 10  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Trim, Viral Protein, Restriction Factor Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Ylinen, A. J. Price, J. Rasaiyaah, S. Hue, N. J. Rose, F. Marzetta, L. C. James, G. J. Towers
Conformational Adaptation Of Asian Macaque Trimcyp Directs Lineage Specific Antiviral Activity.
Plos Pathog. V. 6 1062 2010
PubMed-ID: 20808866  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1001062

(-) Compounds

Molecule 1 - HIV-1 CAPSID
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, RESIDUES 401-564
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 82834
    Strain: LW12.3 ISOLATE
 
Molecule 2 - TRIMCYP
    Chains: B, D
    Fragment: RESIDUES 304-466
    Organism Scientific: MACACA
    Organism Taxid: 9539
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2X83)

(-) Sites  (0, 0)

(no "Site" information available for 2X83)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X83)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:521 -Pro A:522
2Asn C:521 -Pro C:522

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X83)

(-) Exons   (0, 0)

(no "Exon" information available for 2X83)

(-) 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:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x83A00 A:401-546 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x83 A 401 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS 546
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540      


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with B0ZE32_MACFA | B0ZE32 from UniProtKB/TrEMBL  Length:467

    Alignment length:163
                                   313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463   
         B0ZE32_MACFA   304 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFRRIIPGFMCQGGDFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMKRFGSRNGKTSKKITIADCGQL 466
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhhh.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x83 B   2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMKRFGSRNGKTSKKITIADCGQL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   


Chain C from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x83C00 C:401-546 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x83 C 401 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS 546
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540      


Chain D from PDB  Type:PROTEIN  Length:163
 aligned with B0ZE32_MACFA | B0ZE32 from UniProtKB/TrEMBL  Length:467

    Alignment length:163
                                   313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463   
         B0ZE32_MACFA   304 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFRRIIPGFMCQGGDFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMKRFGSRNGKTSKKITIADCGQL 466
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Pro_isomerase-2x83D01 D:7-163                                                                                                                                - Pfam domains (1)
           Pfam domains (2) -----Pro_isomerase-2x83D02 D:7-163                                                                                                                                - Pfam domains (2)
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhhh.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x83 D   2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMKRFGSRNGKTSKKITIADCGQL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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 2X83)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cyclophil-like (65)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain B,D   (B0ZE32_MACFA | B0ZE32)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  Cis Peptide Bonds
    Asn A:521 - Pro A:522   [ RasMol ]  
    Asn C:521 - Pro C:522   [ RasMol ]  
 
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2x82 EVOLUTIONARY BASIS OF HIV RESTRICTION BY THE ANTIRETROVIRAL TRIMCYP