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(-) Description

Title :  CRYSTAL STRUCTURE OF BMJ4 P24 CAPSID PROTEIN IN COMPLEX WITH A10F9 FAB
 
Authors :  Y. Gu, F. Cao, S. Li, Y. A. Yuan, N. Xia
Date :  12 Apr 12  (Deposition) - 17 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  C,D,E,F,H,L
Biol. Unit 1:  C,H,L  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  C,D,E,F,H,L  (1x)
Keywords :  Hiv-1 Capside P24, Capsid Protein, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Gu, F. Cao, S. Li, Y. A. Yuan, N. Xia
Structure Of The Hiv-1 Capsid Protein P24 In Complex With The Broad-Spectrum Antibody A10F9
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - A10F9 FAB HEAVY CHAIN
    Chains: H, E
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - A10F9 FAB LIGHT CHAIN
    Chains: L, F
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - GAG PROTEIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 130-360
    Gene: GAG
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: P24 CAPSID PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : CDEFHL
Biological Unit 1 (1x): C   HL
Biological Unit 2 (1x):  DEF  
Biological Unit 3 (1x): CDEFHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VRL)

(-) Sites  (0, 0)

(no "Site" information available for 3VRL)

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1C:177 -D:177
2C:198 -C:218
3D:198 -D:218
4E:22 -E:96
5E:149 -E:204
6F:23 -F:88
7F:134 -F:194
8H:22 -H:96
9H:149 -H:204
10L:23 -L:88
11L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Phe H:155 -Pro H:156
2Glu H:157 -Pro H:158
3Ser L:7 -Pro L:8
4Glu E:157 -Pro E:158
5Tyr F:140 -Pro F:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VRL)

(-) Exons   (0, 0)

(no "Exon" information available for 3VRL)

(-) 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 C from PDB  Type:PROTEIN  Length:73
 aligned with Q9DGV7_9HIV1 | Q9DGV7 from UniProtKB/TrEMBL  Length:493

    Alignment length:73
                                   287       297       307       317       327       337       347   
         Q9DGV7_9HIV1   278 SILDIKQGPKESFRDYVDRFFKTLRAEQCTQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV 350
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 3vrl C 149 SILDIKQGPKESFRDYVDRFFKTLRAEQCTQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV 221
                                   158       168       178       188       198       208       218   


Chain D from PDB  Type:PROTEIN  Length:73
 aligned with Q9DGV7_9HIV1 | Q9DGV7 from UniProtKB/TrEMBL  Length:493

    Alignment length:73
                                   287       297       307       317       327       337       347   
         Q9DGV7_9HIV1   278 SILDIKQGPKESFRDYVDRFFKTLRAEQCTQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV 350
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 3vrl D 149 SILDIKQGPKESFRDYVDRFFKTLRAEQCTQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV 221
                                   158       168       178       188       198       208       218   


Chain E from PDB  Type:PROTEIN  Length:222
 aligned with A0N7J2_9MURI | A0N7J2 from UniProtKB/TrEMBL  Length:219

    Alignment length:222
                                                                                                                             99    100                                                                                                                    
                                    10        20        30        40        50        60        70        80        90        |-     | 104       114       124       134       144       154       164       174       184       194       204       214  
         A0N7J2_9MURI     1 EVKLVESGGGLVQPGGSLKLSCAASGFTFSSYTMSWIRQTPEKRLEWVAYISDGGGSTYYPDTLKGRFTVSRDNAKNTLYLQMSSLKSEDTAMYYCAIN------FYGMDSWGQGTSVTVSSAKTTPPSVYPMAPGSAAQTNSMVTLGCLVKGYFPEPVAVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vrl E   1 DVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVAIISSGGSYTYYSDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTRDEGNGNYVEAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain F from PDB  Type:PROTEIN  Length:214
 aligned with I6L978_MOUSE | I6L978 from UniProtKB/TrEMBL  Length:234

    Alignment length:214
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
         I6L978_MOUSE    21 DIQLTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSRSGTQFSLKINSLQPEDFGSYYCQHHSGIPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 234
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeeee...ee..........ee...eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrl F   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain H from PDB  Type:PROTEIN  Length:222
 aligned with A0N7J2_9MURI | A0N7J2 from UniProtKB/TrEMBL  Length:219

    Alignment length:222
                                                                                                                             99    100                                                                                                                    
                                    10        20        30        40        50        60        70        80        90        |-     | 104       114       124       134       144       154       164       174       184       194       204       214  
         A0N7J2_9MURI     1 EVKLVESGGGLVQPGGSLKLSCAASGFTFSSYTMSWIRQTPEKRLEWVAYISDGGGSTYYPDTLKGRFTVSRDNAKNTLYLQMSSLKSEDTAMYYCAIN------FYGMDSWGQGTSVTVSSAKTTPPSVYPMAPGSAAQTNSMVTLGCLVKGYFPEPVAVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeee............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vrl H   1 DVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVAIISSGGSYTYYSDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTRDEGNGNYVEAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain L from PDB  Type:PROTEIN  Length:214
 aligned with I6L978_MOUSE | I6L978 from UniProtKB/TrEMBL  Length:234

    Alignment length:214
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
         I6L978_MOUSE    21 DIQLTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSRSGTQFSLKINSLQPEDFGSYYCQHHSGIPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 234
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee......eee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrl L   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 3VRL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain C,D   (Q9DGV7_9HIV1 | Q9DGV7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding 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.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain E,H   (A0N7J2_9MURI | A0N7J2)

Chain F,L   (I6L978_MOUSE | I6L978)

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    Glu H:157 - Pro H:158   [ RasMol ]  
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  Q9DGV7_9HIV1 | Q9DGV7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0N7J2_9MURI | A0N7J2: 2ojz 2ok0
        I6L978_MOUSE | I6L978: 1p7k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VRL)