1QBZ - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF THE SIV GP41 ECTODOMAIN AT 1.47 A

Authors :   Z. -N. Yang, T. C. Mueser, J. Kaufman, S. J. Stahl, P. T. Wingfield, C. C. H

Date :   28 Apr 99 (Deposition) - 17 May 99 (Release) - 16 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.47

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,B,C  (2x)

Keywords :   Siv, Hiv, Gp41, Membrane Fusion, Peptide Inhibitor, Siv Envelope Glycoprotein Gp41, Envelope Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. N. Yang, T. C. Mueser, J. Kaufman, S. J. Stahl, P. T. Wingfield, C. C. Hyde
The Crystal Structure Of The Siv Gp41 Ectodomain At 1. 47 A Resolution.
J. Struct. Biol. V. 126 131 1999
PubMed-ID: 10388624 | Reference-DOI: 10.1006/JSBI.1999.4116

Molecule 1 - PROTEIN (SIV GP41 ECTODOMAIN)
	Cellular Location	:	VIRAL MEMBRANE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SIV GP41 ECTODOMAIN 27-149
	Mutation	:	YES
	Organism Scientific	:	SIMIAN IMMUNODEFICIENCY VIRUS
	Organism Taxid	:	11723
	Strain	:	MAC239

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	HG	2	Ligand/Ion	MERCURY (II) ION
3	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HG	-1	Ligand/Ion	MERCURY (II) ION
3	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HG	-1	Ligand/Ion	MERCURY (II) ION
3	MRD	4	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:41 , MET A:141 , HOH A:8063	BINDING SITE FOR RESIDUE HG A 8001
2	AC2	SOFTWARE	HOH B:8046 , HOH B:8052	BINDING SITE FOR RESIDUE HG B 8002
3	AC3	SOFTWARE	TRP C:98 , ASN C:100 , PRO C:105 , HOH C:8027 , HOH C:8056	BINDING SITE FOR RESIDUE CL C 8003
4	AC4	SOFTWARE	TRP B:98 , ASN B:100 , HOH B:8026	BINDING SITE FOR RESIDUE CL B 8004
5	AC5	SOFTWARE	LYS C:62 , HOH C:8016 , HOH C:8043	BINDING SITE FOR RESIDUE CL C 8005
6	AC6	SOFTWARE	LEU A:56 , TRP A:59 , THR B:111 , LYS B:118 , LYS B:146	BINDING SITE FOR RESIDUE MRD A 7001
7	AC7	SOFTWARE	LEU B:56 , TRP B:59 , THR C:111 , GLU C:114 , TRP C:115 , LYS C:118	BINDING SITE FOR RESIDUE MRD C 7002

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

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

(no "SAP(SNP)/Variant" information available for 1QBZ)

(no "PROSITE Motif" information available for 1QBZ)

(no "Exon" information available for 1QBZ)

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:102
 aligned with Q88018_SIVM3 | Q88018 from UniProtKB/TrEMBL  Length:879

    Alignment length:120
                                   562       572       582       592       602       612       622       632       642       652       662       672
         Q88018_SIVM3   553 QSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKL 672
               SCOP domains d1qbza_ A: Retrovius gp41 protease-resistant core                                                                        SCOP domains
               CATH domains 1qbzA00 A:28-147  [code=1.10.287.210, no name defined]                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qbz A  28 QSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWG------------------TPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKL 147
                                    37        47        57        67        77       | -         -      |107       117       127       137       147
                                                                                    85                104

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q88018_SIVM3 | Q88018 from UniProtKB/TrEMBL  Length:879

    Alignment length:122
                                   562       572       582       592       602       612       622       632       642       652       662       672  
         Q88018_SIVM3   553 QSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 674
               SCOP domains d1qbzb_ B: Retrovius gp41 protease-resistant core                                                                          SCOP domains
               CATH domains 1qbzB00 B:28-149  [code=1.10.287.210, no name defined]                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qbz B  28 QSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWG--------TTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 149
                                    37        47        57        67        77       | -      | 97       107       117       127       137       147  
                                                                                    85       94

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q88018_SIVM3 | Q88018 from UniProtKB/TrEMBL  Length:879

    Alignment length:122
                                   562       572       582       592       602       612       622       632       642       652       662       672  
         Q88018_SIVM3   553 QSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 674
               SCOP domains d1qbzc_ C: Retrovius gp41 protease-resistant core                                                                          SCOP domains
               CATH domains 1qbzC00 C:28-149  [code=1.10.287.210, no name defined]                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qbz C  28 QSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGAAFRQV--TTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 149
                                    37        47        57        67        77        87   |  | 97       107       117       127       137       147  
                                                                                          91 94

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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

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)

Simian immunodeficiency virus [TaxId: 11723] (10)

1a	d1qbza_	A:
1b	d1qbzb_	B:
1c	d1qbzc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

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

Simian immunodeficiency virus. Organism_taxid: 11723. Strain: mac239. (1)

1a	1qbzA00	A:28-147
1b	1qbzB00	B:28-149
1c	1qbzC00	C:28-149

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q88018_SIVM3 | Q88018)

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: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: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: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.

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Description

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Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

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