3MLR - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 2557 IN COMPLEX WITH A NY5 V3 PEPTIDE

Authors :   X. -P. Kong

Date :   18 Apr 10 (Deposition) - 14 Jul 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Human Monoclonal Antibody, Fab, Hiv-1, Gp120, Third Variable Loop, Antibody-Antigen Interaction, 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 - HUMAN MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY 2557 FAB LIGHT CHAIN
	Chains	:	L
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HUMAN MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY 2557 FAB HEAVY CHAIN
	Chains	:	H
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - HIV-1 GP120 THIRD VARIABLE REGION (V3) CROWN
	Chains	:	P
	Organism Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
	Organism Taxid	:	11698
	Strain	:	NEW YORK-5 ISOLATE

		1	2	3
Asymmetric/Biological Unit	:	H	L	P

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3MLR)

(no "Site" information available for 3MLR)

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:196
3	L:23	-	L:88
4	L:138	-	L:197

Asymmetric/Biological Unit

No.	Residues
1	Tyr L:144	-	Pro L:145
2	Phe H:146	-	Pro H:147
3	Glu H:148	-	Pro H:149

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

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

(no "Exon" information available for 3MLR)

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:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee........eeeeehhh.eeeeee...hhhhheeeeeeeeeeee...eeeeeeee...eeeee........eeeeeeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlr H    1 EVQLVESGGEVKQPGQSLKISCKSSGYNFLDSWIGWVRQIPGKGLEWIGIIYPDDSDAHYSPSFEGQVTMSVDKSISTAYLQWTTLQASDTGKYFCTRLYLFEGAQSSNAFDLWGQGTMILVSSGTTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119       129       139       149       159       169       179       189       199       209      
                                                                              52A                            82A||               100A||||||                                                                                                                   
                                                                                                              82B|                100B|||||                                                                                                                   
                                                                                                               82C                 100C||||                                                                                                                   
                                                                                                                                    100D|||                                                                                                                   
                                                                                                                                     100E||                                                                                                                   
                                                                                                                                      100F|                                                                                                                   
                                                                                                                                       100G

Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d3mlrl1 L:1-111 automated matches                                                                                    d3mlrl2 L:112-213 automated matches                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeeeeee......eeeeeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlr L    1 SYDLTQPPSVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGKTATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGDGTRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  213
                                    11        21        31        41        51        61        71        81        91    |||95F       105 |     114       124       134       144       154       164       174       184       194       204         
                                    9|                                                                                  95A|||||        106A                                                                                                           
                                    11                                                                                   95B||||                                                                                                                       
                                                                                                                          95C|||                                                                                                                       
                                                                                                                           95D||                                                                                                                       
                                                                                                                            95E|                                                                                                                       
                                                                                                                             95F

Chain P from PDB  Type:PROTEIN  Length:14
 aligned with ENV_HV1N5 | P12490 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:14
                                   307    
           ENV_HV1N5    298 TKKGIAIGPGRTLY  311
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains GP120-3mlrP01  Pfam domains
         Sec.struct. author ....eeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                3mlr P  303 TKKGIAIGPGRTLY  318
                                  |314    
                                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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

d3mlrl1

L:1-111

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

d3mlrl2

L:112-213

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: GP120] (26)

Family: GP120 (26)

Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1) (1)

GP120-3mlrP01

P:303-318

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (ENV_HV1N5 | P12490)

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: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: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: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: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:144 - Pro L:145	[ RasMol ]

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (4, 4)

Cis Peptide Bonds (3, 3)

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