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Title :   CRYSTAL STRUCTURE OF ANTI-HIV-1 FAB 268-D IN COMPLEX WITH V3 PEPTIDE MN

Authors :   X. P. Kong, V. J. Burke

Date :   18 Mar 09 (Deposition) - 23 Jun 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym./Biol. Unit : H,L,P

Keywords :   Hiv, V3 Loop, Antibody-Antigen Interactions, Aids, Apoptosis, Cell Membrane, Cleavage On Pair Of Basic Residues, Disulfide Bond, Envelope Protein, Fusion Protein, Glycoprotein, Host-Virus Interaction, Membrane, Transmembrane, Viral Immunoevasion, Virion, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Jiang, V. Burke, M. Totrov, C. Williams, T. Cardozo, M. K. Gorny, S. Zolla-Pazner, X. P. Kong
Conserved Structural Elements In The V3 Crown Of Hiv-1 Gp120.
Nat. Struct. Mol. Biol. V. 17 955 2010
PubMed-ID: 20622876 | Reference-DOI: 10.1038/NSMB.1861

Molecule 1 - FAB 268-D, LIGHT CHAIN
	Chains	:	L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	B CELL

Molecule 2 - FAB 268-D, HEAVY CHAIN
	Chains	:	H
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	B CELL

Molecule 3 - ENVELOPE GLYCOPROTEIN GP160
	Chains	:	P
	Engineered	:	YES
	Other Details	:	THE PEPTIDE IS NATURALLY FOUND IN HUMAN IMMUNODEFICIENCY VIRUS 1
	Synonym	:	ENV POLYPROTEIN, SURFACE PROTEIN, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN, TM, GLYCOPROTEIN 41, GP41
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	H	L	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR L:2 , VAL L:3 , ALA L:25 , GLU L:26 , ALA L:27 , HOH L:267	BINDING SITE FOR RESIDUE SO4 L 209
2	AC2	SOFTWARE	ARG L:61 , PRO L:154 , LYS L:156 , HOH L:327 , HOH L:339	BINDING SITE FOR RESIDUE SO4 L 210
3	AC3	SOFTWARE	THR H:57 , ASN H:58 , TYR H:59 , LYS H:64 , HOH H:249 , HOH H:351	BINDING SITE FOR RESIDUE SO4 H 214
4	AC4	SOFTWARE	SER H:127 , SER H:128 , LYS H:129	BINDING SITE FOR RESIDUE SO4 H 215
5	AC5	SOFTWARE	PRO H:185 , SER H:186 , SER H:187 , HOH H:322	BINDING SITE FOR RESIDUE SO4 H 216

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:196
3	L:23	-	L:88
4	L:134	-	L:193

Asymmetric/Biological Unit

No.	Residues
1	Tyr L:140	-	Pro L:141
2	Phe H:146	-	Pro H:147
3	Glu H:148	-	Pro H:149

(no "SAP(SNP)/Variant" information available for 3GO1)

(no "PROSITE Motif" information available for 3GO1)

(no "Exon" information available for 3GO1)

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 H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee......eeeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee...........ee...eeeee........eeeeeeee........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3go1 H    1 EVQLQESGPGLVKPSETLSLTCTVSGGPINNAYWTWIRQPPGKGLEYLGYVYHTGVTNYNPSLKSRLTITIDTSRKQLSLSLKFVTAADSAVYYCAREWAEDGDFGNAFHVWGQGTMVAVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||101       111       121       131       141       151       161       171       181       191       201       211  
                                                                                                            82A||               100A|||||                                                                                                                 
                                                                                                             82B|                100B||||                                                                                                                 
                                                                                                              82C                 100C|||                                                                                                                 
                                                                                                                                   100D||                                                                                                                 
                                                                                                                                    100E|                                                                                                                 
                                                                                                                                     100F

Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee.hhhhh..eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3go1 L    1 SYVLTQPPSVSVSPGQTARITCSAEALSNQYAYWYRQRPGQAPLLIIYKDTKRPSGIPERFSGSTSGTTVTLTISGVQAEDEADYYCQSADSSGDYVFGGGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    11        21        31        41        51        61        71        81        91    |  100      |109       119       129       139       149       159       169       179       189       199         
                                    9|                                                                                  95A        106A                                                                                                      
                                    11

Chain P from PDB  Type:PROTEIN  Length:14
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:14
                                   318    
           ENV_HV1MN    309 RKRIHIGPGRAFYT  322
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                3go1 P  304 RKRIHIGPGRAFYT  319
                                 ||315    
                               309|       
                                312

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 '\|'

(no "SCOP Domain" information available for 3GO1)

(no "CATH Domain" information available for 3GO1)

(no "Pfam Domain" information available for 3GO1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (ENV_HV1MN | P05877)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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/Biological Unit
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 5)

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SS Bonds (4, 4)

Cis Peptide Bonds (3, 3)

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