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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF ANTI-HIV-1 V3 FAB 2219 IN COMPLEX WITH MN PEPTIDE
 
Authors :  R. L. Stanfield, M. K. Gorny, S. Zolla-Pazner, I. A. Wilson
Date :  14 Sep 05  (Deposition) - 04 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Fab-Peptide Complex; Hiv-1; Gp120; V3 Loop, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Stanfield, M. K. Gorny, S. Zolla-Pazner, I. A. Wilson
Crystal Structures Of Human Immunodeficiency Virus Type 1 (Hiv-1) Neutralizing Antibody 2219 In Complex With Three Different V3 Peptides Reveal A New Binding Mode For Hiv-1 Cross-Reactivity.
J. Virol. V. 80 6093 2006
PubMed-ID: 16731948  |  Reference-DOI: 10.1128/JVI.00205-06

(-) Compounds

Molecule 1 - FAB 2219, LIGHT CHAIN
    Cell: PERIPHERAL BLOOD CELLS
    Chains: L
    Fragment: LIGHT CHAIN
    Organ: BLOOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 2219, HEAVY CHAIN
    Cell: PERIPHERAL BLOOD CELLS
    Chains: H
    Fragment: HEAVY CHAIN
    Organ: BLOOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MN PEPTIDE OF EXTERIOR MEMBRANE GLYCOPROTEIN GP120
    Chains: P
    Engineered: YES
    Fragment: RESIDUES 308-325
    Other Details: THIS SEQUENCE OCCURS IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (ISOLATE MN)
    Synonym: GP120
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS L:38 , PRO L:40 , ASP L:85BINDING SITE FOR RESIDUE EDO L 702
2AC2SOFTWAREGLY H:8 , ALA H:9 , ILE H:207 , ASP H:220 , HOH H:772BINDING SITE FOR RESIDUE EDO H 703
3AC3SOFTWAREARG H:38 , SER H:62 , PHE H:63BINDING SITE FOR RESIDUE ACY H 501
4AC4SOFTWAREVAL H:177 , GLN H:179 , SER H:186 , TYR L:178 , SER L:180 , HOH L:717BINDING SITE FOR RESIDUE ACY H 502
5AC5SOFTWAREGLN L:37 , LYS L:45 , LEU L:47 , ILE L:58 , PHE L:62 , HOH L:708BINDING SITE FOR RESIDUE ACY L 503

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:148 -Pro H:149
3Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B0S)

(-) Exons   (0, 0)

(no "Exon" information available for 2B0S)

(-) Sequences/Alignments

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 d2b0sh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                              d2b0sh2 H:114-229 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 2b0sH01 H:1-113 Immunoglobulins                                                                                             2b0sH02 H:114-225 Immunoglobulins                                                                 ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeeeee.........eeeee...eeeeee.......eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b0s H    1 EIQLEQSGAEVKKSGESLKISCQTSGYSFSDYWIGWVRQMPGKGLEWMGIFYPGDSDSRYSPSFEGQVTMSADRSTNTAHLQWSSLKPSDTALYYCARLGGDYEDSGADAFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  229
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119       129||     141       151  |||| 166  ||   177  ||   188       198 |||   211       221||    
                                                                              52A                            82A||               100A||||||                           130|                  154|||    169|      180|               200||              222|    
                                                                                                              82B|                100B|||||                            133                   156||     171       182                203|               225    
                                                                                                               82C                 100C||||                                                   157|                                   205                      
                                                                                                                                    100D|||                                                    162                                                            
                                                                                                                                     100E||                                                                                                                   
                                                                                                                                      100F|                                                                                                                   
                                                                                                                                       100G                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2b0sL01 L:2-107 Immunoglobulins                                                                                 2b0sL02 L:108-211 Immunoglobulins                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeeee......eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b0s L    1 QSVLTQPPSASGTPGQRISISCSGTSSNVENNYVYWYQHLPGTAPKLLIYRNDHRSSGIPDRFSASKSGTSASLAISGLRPEDEGDYYCAAWDDSRGGPDWVFGGGTKLTVLAQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  212
                                    11        21      ||29        39        49        59        69        79        89      |95D       105 |     114       124       134       144       154       164   ||  175       185       195    || 207     
                                    9|              27A|                                                                  95A|||        106A                                                           168|                           200|         
                                    11               27B                                                                   95B||                                                                        170                            203         
                                                                                                                            95C|                                                                                                                   
                                                                                                                             95D                                                                                                                   


Chain P from PDB  Type:PROTEIN  Length:16
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:16
                                   317      
           ENV_HV1MN    308 KRKRIHIGPGRAFYTT  323
               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
                2b0s P  303 KRKRIHIGPGRAFYTT  320
                                  |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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B0S)

(-) Gene Ontology  (22, 22)

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.

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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 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk

(-) Related Entries Specified in the PDB File

2b1a THE SAME FAB COMPLEXES WITH UG1033 PEPTIDE
2b1h THE SAME FAB COMPLEXES WITH UG29 PEPTIDE