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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN

Authors :   R. L. Stanfield, J. M. Rini, I. A. Wilson

Date :   02 Apr 93 (Deposition) - 31 Oct 93 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : H,J,L,M,P,Q
Biol. Unit 1: H,L,P  (1x)
Biol. Unit 2: J,M,Q  (1x)

Keywords :   Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Rini, R. L. Stanfield, E. A. Stura, P. A. Salinas, A. T. Profy, I. A. Wilson
Crystal Structure Of A Human Immunodeficiency Virus Type 1 Neutralizing Antibody, 50. 1, In Complex With Its V3 Loop Peptide Antigen.
Proc. Natl. Acad. Sci. Usa V. 90 6325 1993
PubMed-ID: 8327513 | Reference-DOI: 10.1073/PNAS.90.13.6325
(for further references see the PDB file header)

Molecule 1 - IGG2A 50.1 FAB (LIGHT CHAIN)
	Chains	:	L, M
	Engineered	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	ASW

Molecule 2 - IGG2A 50.1 FAB (HEAVY CHAIN)
	Chains	:	H, J
	Engineered	:	YES

Molecule 3 - HIV-1 V3 LOOP PEPTIDE ANTIGEN
	Chains	:	P, Q
	Engineered	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	H	J	L	M	P	Q
Biological Unit 1 (1x)	:	H		L		P
Biological Unit 2 (1x)	:		J		M		Q

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1GGI)

(no "Site" information available for 1GGI)

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	J:22	-	J:92
4	J:142	-	J:208
5	L:23	-	L:88
6	L:134	-	L:194
7	M:23	-	M:88
8	M:134	-	M:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Asn L:76	-	Pro L:77
3	Asp L:94	-	Pro L:95
4	Tyr L:140	-	Pro L:141
5	Phe H:148	-	Pro H:149
6	Glu H:150	-	Pro H:151
7	Trp H:199	-	Pro H:200
8	Ser M:7	-	Pro M:8
9	Asn M:76	-	Pro M:77
10	Asp M:94	-	Pro M:95
11	Tyr M:140	-	Pro M:141
12	Phe J:148	-	Pro J:149
13	Glu J:150	-	Pro J:151
14	Trp J:199	-	Pro J:200

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

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

(no "Exon" information available for 1GGI)

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 H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1ggih1 H:1-112 Immunoglobulin heavy chain variable domain, VH                                                    d1ggih2 H:113-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1ggiH01 H:1-113 Immunoglobulins                                                                                    1ggiH02 H:114-226 Immunoglobulins                                                                 -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee.........eeeeeee......eeeeeee....eee.......eeeeeehhh...............eeeeeee.........eeeee........eeeee..........eeeeeeeeeee.....eeee........eeeeeeee....eeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ggi H   1 QVQLKESGPGILQPSQTLSLTCSFSGFSLSTYGMGVSWIRQPSGKGLEWLAHIFWDGDKRYNPSLKSRLKISKDTSNNQVFLKITSVDTADTATYYCVQEGYIYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    10        20        30     || 38        48        58        68        78    ||| 85        95 ||    108       118       128 ||    140       150   ||||165   ||  176   ||  188       199||   ||211       221 ||  
                                                             35A|                                             82A||             97|                          130|                  154|||    169|      180|          196| || 206|            223|  
                                                              35B                                              82B|             101                           133                   156||     171       183           198 ||  208             226  
                                                                                                                82C                                                                  157|                               200|                       
                                                                                                                                                                                      162                                202

Chain J from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1ggij1 J:1-112 Immunoglobulin heavy chain variable domain, VH                                                    d1ggij2 J:113-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1ggiJ01 J:1-113 Immunoglobulins                                                                                    1ggiJ02 J:114-227 Immunoglobulins                                                                  - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeeee.....eeeeeee....eee...hhh.eeeeee....eeeeee...hhhh.eeeeeee.........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ggi J   1 QVQLKESGPGILQPSQTLSLTCSFSGFSLSTYGMGVSWIRQPSGKGLEWLAHIFWDGDKRYNPSLKSRLKISKDTSNNQVFLKITSVDTADTATYYCVQEGYIYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    10        20        30     || 38        48        58        68        78    ||| 85        95 ||    108       118       128 ||    140       150   ||||165   ||  176   ||  188       199||   ||211       221 ||  
                                                             35A|                                             82A||             97|                          130|                  154|||    169|      180|          196| || 206|            223|  
                                                              35B                                              82B|             101                           133                   156||     171       183           198 ||  208             226  
                                                                                                                82C                                                                  157|                               200|                       
                                                                                                                                                                                      162                                202

Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1ggil1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1ggil2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1ggiL01 L:1-107 Immunoglobulins                                                                                1ggiL02 L:108-211 Immunoglobulins                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...........eeeeee.....eeeeee...ee.......eeeeee..eeeeee.........eeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ggi L   1 DIVLTQSPGSLAVSLGQRATISCRASESVDDDGNSFLHWYQQKPGQPPKLLIYRSSNLISGIPDRFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPLTFGAGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206     
                                                     27A|||                                                                                                                                                                                        
                                                      27B||                                                                                                                                                                                        
                                                       27C|                                                                                                                                                                                        
                                                        27D

Chain M from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1ggim1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1ggim2 M:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1ggiM01 M:1-108 Immunoglobulins                                                                                 1ggiM02 M:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...........eeeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeeeeeee....eeeeeeeeeeehhhhh....eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ggi M   1 DIVLTQSPGSLAVSLGQRATISCRASESVDDDGNSFLHWYQQKPGQPPKLLIYRSSNLISGIPDRFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPLTFGAGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206     
                                                     27A|||                                                                                                                                                                                        
                                                      27B||                                                                                                                                                                                        
                                                       27C|                                                                                                                                                                                        
                                                        27D

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:17
                                   310       
            ENV_HV1MN   301 CTRPNYNKRKRIHIGPG 317
               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
                 1ggi P 311 C--------KRIHIGPG 321
                            |      312   ||  
                            |      312 316|  
                          311           319

Chain Q from PDB  Type:PROTEIN  Length:9
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:17
                                   310       
            ENV_HV1MN   301 CTRPNYNKRKRIHIGPG 317
               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
                 1ggi Q 311 C--------KRIHIGPG 321
                            |      312   ||  
                            |      312 316|  
                          311           319

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1ggiL02	L:108-211
1b	1ggiL01	L:1-107
1c	1ggiM01	M:1-108
1d	1ggiJ02	J:114-227
1e	1ggiH02	H:114-226
1f	1ggiH01	H:1-113
1g	1ggiJ01	J:1-113
1h	1ggiM02	M:109-211

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

Asymmetric Unit(hide GO term definitions)

Chain P,Q (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 Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ggi)

	Sites
(no "Sites" information available for 1ggi)

	Cis Peptide Bonds
		Asn L:76 - Pro L:77	[ RasMol ]
		Asn M:76 - Pro M:77	[ RasMol ]
		Asp L:94 - Pro L:95	[ RasMol ]
		Asp M:94 - Pro M:95	[ RasMol ]
		Glu H:150 - Pro H:151	[ RasMol ]
		Glu J:150 - Pro J:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Phe J:148 - Pro J:149	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]
		Trp H:199 - Pro H:200	[ RasMol ]
		Trp J:199 - Pro J:200	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr M:140 - Pro M:141	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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(no "Related Entries Specified in the PDB File" available for 1GGI)

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SS Bonds (8, 8)

Cis Peptide Bonds (14, 14)

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