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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION NMR STRUCTURE OF ECTODOMAIN OF SIV GP41, MODELS 21-30 OF AN ENSEMBLE OF 40 SIMULATED ANNEALING STRUCTURES

Authors :   M. Caffrey, A. M. Gronenborn, G. M. Clore

Date :   20 May 98 (Deposition) - 14 Oct 98 (Release) - 24 Nov 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (10x)
NMR Structure *: A,B,C  (1x)

Keywords :   Virus Envelope Protein, Siv Gp41 Ectodomain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Caffrey, M. Cai, J. Kaufman, S. J. Stahl, P. T. Wingfield, D. G. Covell, A. M. Gronenborn, G. M. Clore
Three-Dimensional Solution Structure Of The 44 Kda Ectodomain Of Siv Gp41.
Embo J. V. 17 4572 1998
PubMed-ID: 9707417 | Reference-DOI: 10.1093/EMBOJ/17.16.4572
(for further references see the PDB file header)

Molecule 1 - GP41
	Chains	:	A, B, C
	Fragment	:	ECTODOMAIN, RESIDUES 27 - 149, NUMBERED 1 - 123
	Organism Scientific	:	SIMIAN IMMUNODEFICIENCY VIRUS
	Organism Taxid	:	11723
	Strain	:	SOOTEY MANGABEY

		1	2	3
NMR Structure (10x)	:	A	B	C
NMR Structure * (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2EZR)

(no "Site" information available for 2EZR)

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

(no "Cis Peptide Bond" information available for 2EZR)

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

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

(no "Exon" information available for 2EZR)

NMR Structure

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:123
 aligned with Q88033_SIV | Q88033 from UniProtKB/TrEMBL  Length:879

    Alignment length:123
                                   561       571       581       591       601       611       621       631       641       651       661       671   
           Q88033_SIV   552 AQSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 674
               SCOP domains d2ezra_ A: Retrovius gp41 protease-resistant core                                                                           SCOP domains
               CATH domains 2ezrA00 A:1-123  [code=1.10.287.210, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezr A   1 AQSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGAAFRQVAHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with Q88033_SIV | Q88033 from UniProtKB/TrEMBL  Length:879

    Alignment length:123
                                   561       571       581       591       601       611       621       631       641       651       661       671   
           Q88033_SIV   552 AQSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 674
               SCOP domains d2ezrb_ B: Retrovius gp41 protease-resistant core                                                                           SCOP domains
               CATH domains 2ezrB00 B:1-123  [code=1.10.287.210, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezr B   1 AQSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGAAFRQVAHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with Q88033_SIV | Q88033 from UniProtKB/TrEMBL  Length:879

    Alignment length:123
                                   561       571       581       591       601       611       621       631       641       651       661       671   
           Q88033_SIV   552 AQSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 674
               SCOP domains d2ezrc_ C: Retrovius gp41 protease-resistant core                                                                           SCOP domains
               CATH domains 2ezrC00 C:1-123  [code=1.10.287.210, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezr C   1 AQSRTLLAGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGAAFRQVAHTTVPWPNASLTPKWNNETWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNS 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 '\|'

NMR Structure

Classes(

)

Folds(

)

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	d2ezra_	A:
1b	d2ezrb_	B:
1c	d2ezrc_	C:

NMR Structure

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: sootey mangabey (6)

1a	2ezrA00	A:1-123
1b	2ezrB00	B:1-123
1c	2ezrC00	C:1-123

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

NMR Structure(hide GO term definitions)

Chain A,B,C (Q88033_SIV | Q88033)

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.

NMR Structure
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