1P5A - JenaLib

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Title :   CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN LIPID DETERGENT AND AQUEOUS ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY

Authors :   L. M. Gordon, P. W. Mobley, W. Lee, S. Eskandari, Y. N. Kaznessis, M. A. Sherman, A. J. Waring

Date :   25 Apr 03 (Deposition) - 20 May 03 (Release) - 24 Feb 09 (Revision)

Method :   INFRARED SPECTROSCOPY

Resolution :   NOT APPLICABLE

Chains :   Asym. Unit : A  (19x)
Biol. Unit 1: A  (1x)

Keywords :   Human Immunodeficiency Virus (Hiv-1), Viral Fusion Peptide, Gp41, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. M. Gordon, P. W. Mobley, W. Lee, S. Eskandari, Y. N. Kaznessis, M. A. Sherman, A. J. Waring
Conformational Mapping Of The N-Terminal Peptide Of Hiv-1 Gp41 In Lipid Detergent And Aqueous Environments Using 13C-Enhanced Fourier Transform Infrared Spectroscopy.
Protein Sci. V. 13 1012 2004
PubMed-ID: 15044732 | Reference-DOI: 10.1110/PS.03407704
(for further references see the PDB file header)

Molecule 1 - ENVELOPE POLYPROTEIN GP160
	Chains	:	A
	Engineered	:	YES
	Fragment	:	RESIDUES 519-541
	Other Details	:	C-TERMINUS HAS BEEN AMIDATED
	Other Details - Source	:	THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS GLYCOPROTEIN 41.
	Synonym	:	N-TERMINAL FUSION PEPTIDE OF HIV-1 GP41
	Synthetic	:	YES

		1
Asymmetric Unit (19x)	:	A
Biological Unit 1 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:23	BINDING SITE FOR RESIDUE NH2 A 24

(no "SS Bond" information available for 1P5A)

(no "Cis Peptide Bond" information available for 1P5A)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ENV_HV1BR_005 *	R	538	A	ENV_HV1BR	---	---	A	R	22	A
	* ID not provided by source

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ENV_HV1BR_005 *	R	538	A	ENV_HV1BR	---	---	A	R	22	A
	* ID not provided by source

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

(no "PROSITE Motif" information available for 1P5A)

(no "Exon" information available for 1P5A)

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:24
 aligned with ENV_HV1BR | P03377 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:24
                                   526       536    
            ENV_HV1BR   517 AVGIGALFLGFLGAAGSTMGARSM 540
               SCOP domains d1p5aa_ A:               SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ..hhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------A-- SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 1p5a A   1 AVGIGALFLGFLGAAGSTMGARSx  24
                                    10        20   |
                                                  24-NH2

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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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Peptides (792)

Fold: HIV-1 gp41 fragments (14)

Superfamily: HIV-1 gp41 fragments (14)

Family: HIV-1 gp41 fragments (14)

Protein domain: N-Terminal fusion peptide (1)

Synthetic (1)

d1p5aa_

(no "CATH Domain" information available for 1P5A)

(no "Pfam Domain" information available for 1P5A)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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	ENV_HV1BR \| P03377	:	1env 1erf 1fav 1u6u 1u6v 2zzo 3g9r 3mnw 3vgx 3vtp

1erf	CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY

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