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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 CAPSID PROTEIN C-TERMINAL DOMAIN (146-231) IN COMPLEX WITH A CAMELID VHH.
 
Authors :  S. Igonet, M. -C. Vaney, V. Bartonova, J. Helma, U. Rothbauer, H. Leonha E. Stura, H. -G. Krausslich, F. A. Rey
Date :  03 Oct 10  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Igonet, M. -C. Vaney, V. Bartonova, J. Helma, U. Rothbauer, H. Leonhardt, E. Stura, H. -G. Krausslich, F. A. Rey
Targeting Hiv-1 Virion Formation With Nanobodies - Implications For The Design Of Assembly Inhibitors
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GAG POLYPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIL
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 146-231
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: NL4-3
    Synonym: HIV-1 CAPSID PROTEIN
 
Molecule 2 - CAMELID VHH 9
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: ALPACA
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:202 , GLY A:206 , PRO A:207 , GLY A:208 , ALA A:209 , LEU A:231 , HOH A:2090BINDING SITE FOR RESIDUE GOL A1232
2AC2SOFTWARETYR B:59 , LYS B:64 , GLY B:65 , ARG B:66 , PHE B:67 , THR B:68 , HOH B:2141BINDING SITE FOR RESIDUE GOL B1114

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:22 -B:92
2B:22 -B:92

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:146 -Pro A:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XT1)

(-) Exons   (0, 0)

(no "Exon" information available for 2XT1)

(-) 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:86
 aligned with Q71B32_9HIV1 | Q71B32 from UniProtKB/TrEMBL  Length:231

    Alignment length:86
                                   155       165       175       185       195       205       215       225      
         Q71B32_9HIV1   146 SPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL 231
               SCOP domains d2xt1a_ A: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2xt1 A 146 SPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 231
                                   155       165       175       185       195       205       215       225      


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d2xt1b_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..eeee....eeeeeeee.......eeeeeee......eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2xt1 B   0 AQVQLVESGGGLVQAGGSLRLSCAASGSFFMSNVMAWYRQAPGKARELIAAIRGGDMSTVYDDSVKGRFTITRDDDKNILYLQMNDLKPEDTAMYYCKASGSSWGQGTQVTVSS 113
                                     9        19        29        39        49   |    58        68        78    ||| 85        95||     109    
                                                                               52A                            82A||            96|            
                                                                                                               82B|            101            
                                                                                                                82C
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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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XT1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q71B32_9HIV1 | Q71B32)
biological process
    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:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2xv6 CRYSTAL STRUCTURE OF THE HIV-1 CAPSID PROTEIN C- TERMINAL DOMAIN (146-220) IN COMPLEX WITH A CAMELID VHH.
2xxc CRYSTAL STRUCTURE OF A CAMELID VHH RAISED AGAINST THE HIV-1 CAPSID PROTEIN C-TERMINAL DOMAIN.
2xxm CRYSTAL STRUCTURE OF THE HIV-1 CAPSID PROTEIN C- TERMINAL DOMAIN IN COMPLEX WITH A CAMELID VHH AND THE CAI PEPTIDE.