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(-) Description

Title :  STRUCTURE OF HIV-1 GP41 NHR/FUSION INHIBITOR COMPLEX P21
 
Authors :  X. Yao, S. Waltersperger, M. T. Wang, S. Cui
Date :  23 Aug 11  (Deposition) - 13 Jun 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  6-Helix Bundle, Membrane Fusion Inhibition, Membrane Protein- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yao, H. Chong, C. Zhang, Z. Qiu, B. Qin, R. Han, S. Waltersperger, M. T. Wang, Y. He, S. Cui
Structural Basis Of Potent And Broad Hiv-1 Fusion Inhibitor Cp32M
J. Biol. Chem. V. 287 26618 2012
PubMed-ID: 22679024  |  Reference-DOI: 10.1074/JBC.M112.381079

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    ChainsA, C, E
    EngineeredYES
    FragmentNHR (UNP RESIDUES (546-588)
    Organism CommonHIV-1
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid11676
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY.
    SynonymENV POLYPROTEIN, SURFACE PROTEIN GP120, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN GP41, TM, GLYCOPROTEIN 41, GP41
    SyntheticYES
 
Molecule 2 - CP32M
    ChainsB, D, F
    EngineeredYES
    Other DetailsTHIS SEQUENCE DOES NOT OCCUR NATURALLY, BUT DESIGNED BASED ON SEQUENCE OF HIV-1 GP41 CHR 621-652.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:564 , HOH E:1206BINDING SITE FOR RESIDUE MG E 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VH7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn B:624 -Glu B:625

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VH7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VH7)

(-) Exons   (0, 0)

(no "Exon" information available for 3VH7)

(-) 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 A from PDB  Type:PROTEIN  Length:52
 aligned with ENV_HV1B1 | P03375 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:88
                                   522       532       542       552       562       572       582       592        
           ENV_HV1B1    513 VGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSG  600
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh--------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------hh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                3vh7 A   -6 ADIGSEF--------------------------SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLK----------SG 1001
                                  |  -         -         -   |   552       562       572       582     |   -      | 
                                  0                        546                                       588       1000 

Chain B from PDB  Type:PROTEIN  Length:30
                                                               
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                3vh7 B  622 EWNEMTWMEWEREIENYTKLIYKILEESQE  651
                                   631       641       651

Chain C from PDB  Type:PROTEIN  Length:51
 aligned with ENV_HV1B1 | P03375 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:114
                                   483       493       503       513       523       533       543       553       563       573       583    
           ENV_HV1B1    474 DMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYL  587
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhh-------------------------------------hhhhh--------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                3vh7 C   -8 AMAD-------------------------------------IGSEF--------------------------SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYL  587
                               |     -         -         -         - |   |   -         -         -  |    553       563       573       583    
                              -5                                    -4   0                        546                                         

Chain D from PDB  Type:PROTEIN  Length:31
                                                                
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                3vh7 D  621 VEWNEMTWMEWEREIENYTKLIYKILEESQE  651
                                   630       640       650 

Chain E from PDB  Type:PROTEIN  Length:56
 aligned with ENV_HV1B1 | P03375 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:77
                                   534       544       554       564       574       584       594       
           ENV_HV1B1    525 AAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGK  601
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh-----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------hhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                3vh7 E   -9 SAMADIGSE-----------FSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLK----------SGG 1002
                                    |-         -||     554       564       574       584   |     -    |  
                                   -1           0|                                       588       1000  
                                               546                                                       

Chain F from PDB  Type:PROTEIN  Length:31
                                                                
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                3vh7 F  621 VEWNEMTWMEWEREIENYTKLIYKILEESQE  651
                                   630       640       650 

   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 3VH7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VH7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VH7)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,E   (ENV_HV1B1 | P03375)
molecular function
    GO:0042609    CD4 receptor binding    Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0044538    host cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures of a host cell.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1B1 | P033752ari 3vgx 3vgy 3vu5 3vu6 3w19

(-) Related Entries Specified in the PDB File

3vgx 3vgy