1FAV - JenaLib

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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   THE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR IN COMPLEX WITH THE HIV-1 GP41 TRIMERIC CORE

Authors :   G. Zhou, M. Ferrer, R. Chopra, T. Strassmaier, W. Weissenhorn, J. J. Ske D. Oprian, S. L. Schreiber, S. C. Harrison, D. C. Wiley

Date :   13 Jul 00 (Deposition) - 23 Aug 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,C
Biol. Unit 1: A,C  (3x)

Keywords :   Hiv-1, Gp41, Inhibitor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Zhou, M. Ferrer, R. Chopra, T. M. Kapoor, T. Strassmaier, W. Weissenhorn, J. J. Skehel, D. Oprian, S. L. Schreiber, S. C. Harrison, D. C. Wiley
The Structure Of An Hiv-1 Specific Cell Entry Inhibitor In Complex With The Hiv-1 Gp41 Trimeric Core.
Bioorg. Med. Chem. V. 8 2219 2000
PubMed-ID: 11026535 | Reference-DOI: 10.1016/S0968-0896(00)00155-3

Molecule 1 - HIV-1 ENVELOPE PROTEIN CHIMERA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Other Details	:	CHIMERA CONSISTS OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP41

Molecule 2 - PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)
	Chains	:	C
	Engineered	:	YES
	Fragment	:	OUTER PEPTIDE OF GP41 OF HIV-1
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HIV-1.
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (3x)	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	3PA	1	Mod. Amino Acid	3-CYCLOPENTYL-PROPIONIC ACID
2	4BA	1	Mod. Amino Acid	4-[(2-CARBOXY-ETHYLAMINO)-METHYL]-BENZOIC ACID
3	GGL	1	Mod. Amino Acid	L-GLUTAMIC ACID

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	3PA	3	Mod. Amino Acid	3-CYCLOPENTYL-PROPIONIC ACID
2	4BA	3	Mod. Amino Acid	4-[(2-CARBOXY-ETHYLAMINO)-METHYL]-BENZOIC ACID
3	GGL	3	Mod. Amino Acid	L-GLUTAMIC ACID

(no "Site" information available for 1FAV)

(no "SS Bond" information available for 1FAV)

(no "Cis Peptide Bond" information available for 1FAV)

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GCN4_YEAST_006 *	D	196	E	GCN4_YEAST	---	---	A	E	19	E
2	UniProt	VAR_ENV_HV1BR_006 *	G	552	D	ENV_HV1BR	---	---	A	G	36	D
	* ID not provided by source

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

Biological Unit 1 (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GCN4_YEAST_006 *	D	196	E	GCN4_YEAST	---	---	A	E	19	E
2	UniProt	VAR_ENV_HV1BR_006 *	G	552	D	ENV_HV1BR	---	---	A	G	36	D
	* ID not provided by source

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BZIP	PS50217	Basic-leucine zipper (bZIP) domain profile.	GCN4_YEAST	231-276	1	A:46-76
2	BZIP_BASIC	PS00036	Basic-leucine zipper (bZIP) domain signature.	GCN4_YEAST	231-245	1	A:46-50

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BZIP	PS50217	Basic-leucine zipper (bZIP) domain profile.	GCN4_YEAST	231-276	3	A:46-76
2	BZIP_BASIC	PS00036	Basic-leucine zipper (bZIP) domain signature.	GCN4_YEAST	231-245	3	A:46-50

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YEL009C	1	YEL009C.1	V:139763-138918	846	GCN4_YEAST	1-281	281	1	A:2-79 (gaps)	103

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
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Chain A from PDB  Type:PROTEIN  Length:78
 aligned with ENV_HV1BR | P03377 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:152
                                   453       463       473       483       493       503       513       523       533       543       553       563       573       583       593  
            ENV_HV1BR   444 ISGQIRCSSNITGLLLTRDGGNNNNGSEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGARSMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQ 595
               SCOP domains d1fav                     .1 A:                 ,C: Re           trovius gp4                         1 protease-resistant core                           SCOP domains
               CATH domains 1favA                     00 A:                 2-79             [code=1.10.                         287.210, no name defined]                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh---------------------hhhhh-----------------hhhhhh-----------hhhhhhhhhhh-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------E-----------------------------------------D------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fav A   2 IEDKI---------------------EEILS-----------------KIYHIE-----------NEIARIKKLIG-------------------------EARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQ  79
                                |    -         -      | 10|        -        13   |     -     |  22     |   -         -         - |      37        47        57        67        77  
                                6                     7  11                12   17          18        28                        29

Chain A from PDB  Type:PROTEIN  Length:78
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:103
                                   177       187       197       207       217       227       237       247       257       267   
           GCN4_YEAST   168 LEDAKLTQTRKVKKPNSVVKKSHHVGKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENE 270
               SCOP domains d1f          av.1 A:,C: Ret rovius g  p4   1 pro tease-resi   stan  t core                              SCOP domains
               CATH domains 1fa          vA00 A:2-79  [ code=1.1  0.   287.2 10, no nam   e de  fined]                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h----------hhhhhhhhhhhhhh-hhhhhhhh--hh---hhhhh-hhhhhhhhhh---hhhh--hhhhhhhhhhhhhhhhhhhhh---hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------E----------------------D--------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------BZIP  PDB: A:46-76 UniProt: 231-276      PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------BZIP_BASIC     ------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-79 (gaps) UniProt: 1-281 [INCOMPLETE]                                                Transcript 1
                 1fav A   2 IED----------KIEEILSKIYHIEN-EIARIKKL--IG---EARQL-LSGIVQQQNN---LLRA--IEAQQHLLQLTVWGIKQLQAR---ILAVERYLKDQ  79
                              |      -   |    11      | 20     |  28   |   |34        |-  |  |  49        59        |-  |     76   
                              4          5           18 |     26 27|  29  33 |       43  44 47 48                  68  69          
                                                       19         28        34

Chain C from PDB  Type:PROTEIN  Length:31
 aligned with ENV_HV1BR | P03377 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:31
                                   647       657       667 
            ENV_HV1BR   638 REINNYTSLIHSLIEESQNQQEKNEQELLEL 668
               SCOP domains d1fav.1 A:,C:                   SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 1fav C 122 xxxNNYTSLIHSLIEESQNQQEKNEQELLEL 152
                            |||    131       141       151 
                          122-3PA                          
                           123-GGL                         
                            124-4BA

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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Coiled coil proteins (689)

Fold: Stalk segment of viral fusion proteins (231)

Superfamily: Virus ectodomain (48)

Family: Virus ectodomain (44)

Protein domain: Retrovius gp41 protease-resistant core (35)

Human immunodeficiency virus type 1 [TaxId: 11676] (23)

d1fav.1

A:,C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.210, no name defined] (35)

Human immunodeficiency virus 1. Organism_taxid: 11676. (9)

1favA00

A:2-79

(no "Pfam Domain" information available for 1FAV)

Asymmetric Unit(hide GO term definitions)

Chain A (GCN4_YEAST | P03069)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0001135	transcription factor activity, RNA polymerase II transcription factor recruiting	The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
	GO:0001084	transcription factor activity, TFIID-class binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001190	transcriptional activator activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	GO:0001191	transcriptional repressor activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0010691	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels	Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0001080	nitrogen catabolite activation of transcription from RNA polymerase II promoter	A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	GO:0045899	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:1903833	positive regulation of cellular response to amino acid starvation	Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain A,C (ENV_HV1BR | P03377)

molecular function
	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.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	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:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	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:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	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:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
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	1fav
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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	GCN4_YEAST \| P03069
		Comparative Protein Structure Models	:	ModBase
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(no "Related Entries Specified in the PDB File" available for 1FAV)

Description

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