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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 2558 IN COMPLEX WITH MN PEPTIDE
 
Authors :  X. P. Kong
Date :  07 Nov 11  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Ig Domains, Antibody Fab, Antigen Binding, The Third Variable Region Of Hiv-1 Gp120, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Gorny, J. Sampson, H. Li, X. Jiang, M. Totrov, X. H. Wang, C. Williams, T. O'Neal, B. Volsky, L. Li, T. Cardozo, P. Nyambi, S. Zolla-Pazner, X. P. Kong
Human Anti-V3 Hiv-1 Monoclonal Antibodies Encoded By The Vh5-51/Vl Lambda Genes Define A Conserved Antigenic Structure.
Plos One V. 6 27780 2011
PubMed-ID: 22164215  |  Reference-DOI: 10.1371/JOURNAL.PONE.0027780

(-) Compounds

Molecule 1 - LIGHT CHAIN OF ANTI-HIV-1 V3 MONOCLONAL ANTIBODY 2558
    Chains: L
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: IMMUNE SYSTEM
 
Molecule 2 - FAB REGION OF THE HEAVY CHAIN OF ANTI-HIV-1 V3 MONOCLONAL ANTIBODY 2558
    Chains: H
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: IMMUNE SYSTEM
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP160
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 306-328
    Organism Common: HIV-1
    Organism Taxid: 11696
    Synonym: ENV POLYPROTEIN, SURFACE PROTEIN GP120, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN GP41, TM, GLYCOPROTEIN 41, GP41
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY L:107 , GLN L:108 , ASN L:170 , HOH L:403BINDING SITE FOR RESIDUE CA L 209
2AC2SOFTWAREASN H:60 , SER H:62 , PHE H:63 , HOH H:231 , HOH H:345 , NAG H:402 , FUC H:403 , TYR L:2 , LEU L:95 , VAL L:96 , HOH L:215 , HOH L:334BINDING SITE FOR RESIDUE NAG H 401
3AC3SOFTWAREHOH H:269 , HOH H:340 , HOH H:354 , NAG H:401 , HOH H:449 , HOH H:630 , TYR L:2 , GLU L:3BINDING SITE FOR RESIDUE NAG H 402
4AC4SOFTWAREARG H:38 , GLU H:46 , PHE H:63 , HOH H:329 , NAG H:401 , HOH H:559BINDING SITE FOR RESIDUE FUC H 403

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Gly H:133 -Gly H:134
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UJI)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3uji H    1 QVQLVQSAAEVKKPGEALKISCKGSGYSFSNYWIAWVRQMPGKGLEWMGIVYPDDSDSSYNSSFQGQITFSADKSISTAYLHWTSLQASDTAMYYCARLGFEGDYSGSFFDYWGQGTLLIVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120      |135       145       155       165       175       185       195       205        
                                                                              52A                            82A||               100A|||||                        127|                                                                                
                                                                                                              82B|                100B||||                         133                                                                                
                                                                                                               82C                 100C|||                                                                                                            
                                                                                                                                    100D||                                                                                                            
                                                                                                                                     100E|                                                                                                            
                                                                                                                                      100F                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee.hhhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3uji L    2 YELTQPPSVSVSPGQTASITCSGDILGDKYVSWYQQKSGQSPLLVIYEDTKRPSGIPDRFSGSKSGNTATLTISGTQAMDEADYYCQAWDSTLGVVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAP  208
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200        
                                   9|                                                                                  95A        106A                                                                                                      
                                   11                                                                                                                                                                                                       


Chain P from PDB  Type:PROTEIN  Length:18
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:18
                                   315        
           ENV_HV1MN    306 YNKRKRIHIGPGRAFYTT  323
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .hhhhh.eee...ee... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                3uji P  301 YNKRKRIHIGPGRAFYTT  320
                                   312        
                                  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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk

(-) Related Entries Specified in the PDB File

3ujj