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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 1006-15D IN COMPLEX WITH AN MN V3 PEPTIDE
 
Authors :  X. -P. Kong
Date :  18 Apr 10  (Deposition) - 14 Jul 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
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

(-) Compounds

Molecule 1 - HUMAN MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY 1006-15D FAB LIGHT CHAIN
    Chains: L, M
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HUMAN MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY 1006-15D FAB HEAVY CHAIN
    Chains: H, I
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HIV-1 GP120 THIRD VARIABLE REGION (V3) CROWN
    Chains: P, Q
    Organism Common: HIV-1
    Organism Taxid: 11696

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HILMPQ
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  I M Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO L:40 , GLY L:41 , SER L:42 , HOH L:229BINDING SITE FOR RESIDUE PO4 L 210
2AC2SOFTWARETYR H:27 , ASP H:31 , HIS H:32 , HIS H:96 , TYR H:100D , PO4 H:217 , ARG P:304BINDING SITE FOR RESIDUE PO4 H 216
3AC3SOFTWAREVAL H:2 , ARG H:94 , HIS H:96 , PO4 H:216 , HOH H:240BINDING SITE FOR RESIDUE PO4 H 217
4AC4SOFTWAREGLU M:83 , VAL M:106 , TYR M:140 , LYS M:166 , TYR M:172 , HOH M:227BINDING SITE FOR RESIDUE PO4 M 210
5AC5SOFTWAREASP I:31 , HIS I:32 , ASP L:151BINDING SITE FOR RESIDUE PO4 I 216
6AC6SOFTWAREASP I:54BINDING SITE FOR RESIDUE PO4 I 217

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3I:22 -I:92
4I:140 -I:196
5L:23 -L:88
6L:134 -L:193
7M:23 -M:88
8M:134 -M:193

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser H:161 -Gly H:162
5Thr P:320 -Lys P:321
6Tyr M:140 -Pro M:141
7Phe I:146 -Pro I:147
8Glu I:148 -Pro I:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MLW)

(-) Sequences/Alignments

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:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeee..ee.....ee.....ee...eeeeee.......eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3mlw H    1 QVQLVQSGAEVKKAGESLEISCKGSGYTFTDHWIAWVRQVPGKGLEWMGMIYPGDSDTRYSPSLQGRVTMSADKTLSTAYLQWSRLEASDTAMYYCARLHYSDRSGSYFNDVFHMWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||    107       117       127       137       147       157       167       177       187       197       207        
                                                                              52A                            82A||               100A||||||||                                                                                                                   
                                                                                                              82B|                100B|||||||                                                                                                                   
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain I from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee..ee.....ee.....ee...eeeeee.......eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3mlw I    1 QVQLVQSGAEVKKAGESLEISCKGSGYTFTDHWIAWVRQVPGKGLEWMGMIYPGDSDTRYSPSLQGRVTMSADKTLSTAYLQWSRLEASDTAMYYCARLHYSDRSGSYFNDVFHMWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||    107       117       127       137       147       157       167       177       187       197       207        
                                                                              52A                            82A||               100A||||||||                                                                                                                   
                                                                                                              82B|                100B|||||||                                                                                                                   
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d3mlwl1 L:1-107 automated matches                                                                                d3mlwl2 L:108-209 automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....eeeeeee..........eeeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeeeee......eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlw L    1 QSVLTQPPSASGTPGQRVTISCSGNSSNIENNYVYWYQQLPGSTPKLLIFRDDQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCASWDDSRGGPDYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                    11        21      ||29        39        49        59        69        79        89      |95D       105 |     114       124       134       144       154       164       174       184       194       204     
                                    9|              27A|                                                                  95A|||        106A                                                                                                       
                                    11               27B                                                                   95B||                                                                                                                   
                                                                                                                            95C|                                                                                                                   
                                                                                                                             95D                                                                                                                   


Chain M from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d3mlwm1 M:1-107 automated matches                                                                                d3mlwm2 M:108-209 automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee......eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee...ee....ee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mlw M    1 QSVLTQPPSASGTPGQRVTISCSGNSSNIENNYVYWYQQLPGSTPKLLIFRDDQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCASWDDSRGGPDYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                    11        21      ||29        39        49        59        69        79        89      |95D       105 |     114       124       134       144       154       164       174       184       194       204     
                                    9|              27A|                                                                  95A|||        106A                                                                                                       
                                    11               27B                                                                   95B||                                                                                                                   
                                                                                                                            95C|                                                                                                                   
                                                                                                                             95D                                                                                                                   


Chain P from PDB  Type:PROTEIN  Length:17
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:17
                                   317       
           ENV_HV1MN    308 KRKRIHIGPGRAFYTTK  324
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ....eeee..eee.... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                3mlw P  303 KRKRIHIGPGRAFYTTK  321
                                  |314       
                                309|         
                                 312         


Chain Q from PDB  Type:PROTEIN  Length:17
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:17
                                   316       
           ENV_HV1MN    307 NKRKRIHIGPGRAFYTT  323
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
           Pfam domains (1) GP120-3mlwQ01     Pfam domains (1)
           Pfam domains (2) GP120-3mlwQ02     Pfam domains (2)
         Sec.struct. author .....eeee..eee... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                3mlw Q  302 NKRKRIHIGPGRAFYTT  320
                                   313       
                                 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (22, 22)

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.

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  3mlw
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  ENV_HV1MN | P05877
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENV_HV1MN | P05877: 1acy 1ai1 1f58 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk

(-) Related Entries Specified in the PDB File

3mlr 3mls 3mlt 3mlu 3mlv 3mlx 3mly 3mlz