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Title :   HIV-1 CAPSID C-TERMINAL DOMAIN IN COMPLEX WITH AN INHIBITOR OF PARTICLE ASSEMBLY

Authors :   F. Ternois, J. Sticht, S. Duquerroy, H. -G. Krausslich, F. A. Rey

Date :   17 Jun 05 (Deposition) - 21 Jul 05 (Release) - 15 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,T

Keywords :   Viral Protein/Peptide, Hiv, Capsid, Inhibitor, Assembly, Polyprotein, Complex (Viral Protein/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Ternois, J. Sticht, S. Duquerroy, H. -G. Krausslich, F. A. Rey
The Hiv-1 Capsid Protein C-Terminal Domain In Complex With A Virus Assembly Inhibitor
Nat. Struct. Mol. Biol. V. 12 678 2005
PubMed-ID: 16041386 | Reference-DOI: 10.1038/NSMB967
(for further references see the PDB file header)

Molecule 1 - HIV-1 CAPSID PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	C-TERMINAL DOMAIN, RESIDUES 278-363
	Organism Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	NL4-3

Molecule 2 - INHIBITOR OF CAPSID ASSEMBLY
	Chains	:	T
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:166 , TYR A:169 , LYS A:170 , HOH A:2113	BINDING SITE FOR RESIDUE ACY A1231

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:223	-	Pro A:224
2	Gly T:11	-	Pro T:12

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GAG_HV1B1_001 *	V	297	L	GAG_HV1B1	---	---	A	V	165	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 2BUO)

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:85
 aligned with GAG_HV1B1 | P03347 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:85
                                   288       298       308       318       328       338       348       358     
            GAG_HV1B1   279 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL 363
               SCOP domains d2buoa_ A: automated matches                                                          SCOP domains
               CATH domains 2buoA00 A:147-231  [code=1.10.1200.30, no name defined]                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------L------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2buo A 147 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 231
                                   156       166       176       186       196       206       216       226

Chain A from PDB  Type:PROTEIN  Length:85
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:85
                                   288       298       308       318       328       338       348       358     
         Q72497_9HIV1   279 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 363
               SCOP domains d2buoa_ A: automated matches                                                          SCOP domains
               CATH domains 2buoA00 A:147-231  [code=1.10.1200.30, no name defined]                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------L------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2buo A 147 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 231
                                   156       166       176       186       196       206       216       226

Chain T from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2buo T   1 ITFEDLLDYYGP  12
                                    10

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Acyl carrier protein-like (148)

Superfamily: Retrovirus capsid dimerization domain-like (45)

Family: Retrovirus capsid protein C-terminal domain (31)

Protein domain: automated matches (12)

Human immunodeficiency virus 1 [TaxId: 11676] (4)

d2buoa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A (155)

Homologous Superfamily: [code=1.10.1200.30, no name defined] (18)

Hiv-1 (Human immunodeficiency virus 1) (1)

2buoA00

A:147-231

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GAG_HV1B1 | P03347)

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: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: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:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	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:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0072494	host multivesicular body	A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain A (Q72497_9HIV1 | Q72497)

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: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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:223 - Pro A:224	[ RasMol ]
		Gly T:11 - Pro T:12	[ RasMol ]

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1l6n	STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG POLYPROTEIN
1m9c	X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN (1-146) M-TYPE COMPLEX.
1m9d	X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN (1-146) O-TYPE CHIMERA COMPLEX.
1m9e	X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN (1-146) M-TYPE H87A COMPLEX.
1m9f	X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN (1-146) M-TYPE H87A,A88M COMPLEX.
1m9x	X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN (1-146) M-TYPE H87A,A88M,G89A COMPLEX.
1m9y	X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN (1-146) M-TYPE H87A,G89A COMPLEX.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (21, 36)

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