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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM
 
Authors :  A. Carfi, S. H. Willis, J. C. Whitbeck, C. Krummenacker, G. H. Cohen, R. J. Eisenberg, D. C. Wiley
Date :  17 Jul 01  (Deposition) - 26 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  V-Type Ig Molecule And Tnfr Superfamily, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Carfi, S. H. Willis, J. C. Whitbeck, C. Krummenacher, G. H. Cohen, R. J. Eisenberg, D. C. Wiley
Herpes Simplex Virus Glycoprotein D Bound To The Human Receptor Hvea.
Mol. Cell V. 8 169 2001
PubMed-ID: 11511370  |  Reference-DOI: 10.1016/S1097-2765(01)00298-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HERPESVIRUS ENTRY MEDIATOR
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentHVEA-162
    MutationYES
    Organism CommonHERPES SIMPLEX VIRUS TYPE 1
    Organism ScientificHUMAN HERPESVIRUS 1
    Organism Taxid10298
 
Molecule 2 - GLYCOPROTEIN D
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentGD-285
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:41 , ASN A:94 , ASN A:171 , NAG A:367BINDING SITE FOR RESIDUE NAG A 366
2AC2SOFTWARETYR A:2 , NAG A:366BINDING SITE FOR RESIDUE NAG A 367
3AC3SOFTWAREPRO A:31 , ARG A:130BINDING SITE FOR RESIDUE SO4 A 525
4AC4SOFTWAREPRO B:42 , GLY B:43 , THR B:44 , CYS B:58 , CYS B:73BINDING SITE FOR RESIDUE SO4 B 526
5AC5SOFTWARELYS A:190 , TYR A:191BINDING SITE FOR RESIDUE SO4 A 527
6AC6SOFTWAREMET A:102 , LEU A:165 , GLN A:178 , HOH A:546BINDING SITE FOR RESIDUE SO4 A 528
7AC7SOFTWAREILE B:90 , CYS B:100 , ARG B:101BINDING SITE FOR RESIDUE SO4 B 529

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:189
2A:106 -A:202
3A:118 -A:127
4B:4 -B:15
5B:16 -B:29
6B:19 -B:37
7B:40 -B:55
8B:58 -B:73
9B:61 -B:81
10B:83 -B:100
11B:89 -B:97

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:243 -Pro A:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018955A117TTNR14_HUMANPolymorphism2234163BA79T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNR14_HUMAN41-75
77-119
  1-
B:39-81
2TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR14_HUMAN78-119  1B:40-81

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003557163aENSE00001409963chr1:2487805-2488172368TNR14_HUMAN1-23230--
1.4bENST000003557164bENSE00001035641chr1:2489165-2489273109TNR14_HUMAN24-60371B:4-2219
1.5aENST000003557165aENSE00001734381chr1:2489782-2489907126TNR14_HUMAN60-102431B:22-6443
1.5jENST000003557165jENSE00001345049chr1:2491262-2491417156TNR14_HUMAN102-154531B:64-105 (gaps)42
1.6bENST000003557166bENSE00002186068chr1:2492063-249215391TNR14_HUMAN154-184310--
1.6iENST000003557166iENSE00002149536chr1:2493112-2493254143TNR14_HUMAN184-232490--
1.6lENST000003557166lENSE00001035623chr1:2494304-249433532TNR14_HUMAN232-242110--
1.6pENST000003557166pENSE00001922328chr1:2494587-2495268682TNR14_HUMAN243-283410--

(-) 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:259
 aligned with GD_HHV1P | P57083 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:259
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275         
             GD_HHV1P    26 KYALADASLKMADPNRFRGKDLPVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSE 284
               SCOP domains d1jmaa_ A: HSV glycoprotein D                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1jmaA00 A:1-259  [code=2.70.230.10, no name defined]                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------Herpes_glycop_D-1jmaA01 A:57-181                                                                                             ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh...............ee......eee..................eeeeeee.....eeee....hhhhhhhh.hhhhhh..eeeeeeeeeee..eeeeeeeeeeeee..........eee..ee......eee......eeee..hhhhheeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhh.........ee..hhhhhhhhhhhhhhh.........ee....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jma A   1 KYALADASLKMADPNRFRGKDLPVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSE 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with TNR14_HUMAN | Q92956 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:102
                                    51        61        71        81        91       101       111       121       131       141  
          TNR14_HUMAN    42 CKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAYAT 143
               SCOP domains d1jmab1 B:4-59 Cellular receptor HveA                   d1jmab2 B:60-105 Cellular recepto  r HveA      SCOP domains
               CATH domains 1jmaB01 B:4-57                                        1jmaB02 B:58-105                                 CATH domains
               Pfam domains ------------------------------------TNFR_c6-1jmaB01 B:40-81                   ------------------------ Pfam domains
         Sec.struct. author ...................eeeee........eeee....ee..........ee.........eeeee........eeee...eeeee.--....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------T-------------------------- SAPs(SNPs)
                PROSITE (1) TNFR_NGFR_2  PDB: - UniProt: 41-75-TNFR_NGFR_2  PDB: B:39-81 UniProt: 77-119  ------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------TNFR_NGFR_1  PDB: B:40-81 UniProt: 78-119 ------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.4b          -----------------------------------------Exon 1.5j  PDB: B:64-105 (gaps)            Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.5a  PDB: B:22-64 UniProt: 60-102    ----------------------------------------- Transcript 1 (2)
                 1jma B   4 CKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQ--DHCAACRAYAT 105
                                    13        23        33        43        53        63        73        83        |- |     103  
                                                                                                                   92 95          

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (33, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GD_HHV1P | P57083)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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: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.

Chain B   (TNR14_HUMAN | Q92956)
molecular function
    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:0005031    tumor necrosis factor-activated receptor activity    Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0046642    negative regulation of alpha-beta T cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell proliferation.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:2000406    positive regulation of T cell migration    Any process that activates or increases the frequency, rate or extent of T cell migration.
    GO:0002741    positive regulation of cytokine secretion involved in immune response    Any process that activates or increases the frequency, rate, or extent of cytokine secretion contributing to an immune response.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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.
cellular component
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GD_HHV1P | P570831l2g 2c36 2c3a
        TNR14_HUMAN | Q929562aw2 4fhq 4rsu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JMA)