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(-) Description

Title :  LMP1 PROTEIN BINDS TO TRAF3 AS A STRUCTURAL CD40
 
Authors :  S. D. Wu, P. Xie, K. Welsh, C. Li, C. -Z. Ni, X. Zhu, J. C. Reed, A. C. Satterthwait, G. A. Bishop, K. R. Ely
Date :  10 May 05  (Deposition) - 19 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Cd40, Nf-Kb Signaling, Lmp1, Tnf Receptor, Traf3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. D. Wu, P. Xie, K. Welsh, C. Li, C. -Z. Ni, X. Zhu, J. C. Reed, A. C. Satterthwait, G. A. Bishop, K. R. Ely
Lmp1 Protein From The Epstein Barr Virus Is A Structural Cd40 Decoy In B Lymphocytes Fro Binding To Traf3
J. Biol. Chem. V. 39 33620 2005
PubMed-ID: 16009714  |  Reference-DOI: 10.1074/JBC.M502511200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TNF RECEPTOR ASSOCIATED FACTOR 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET21B
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 377-568
    GeneTRAF3, CAP1, CRAF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD40 RECEPTOR ASSOCIATED FACTOR 1, CRAF1, CD40 BINDING PROTEIN, CD40BP, LMP1 ASSOCIATED PROTEIN, LAP1, CAP-1
 
Molecule 2 - LATENT MEMBRANE PROTEIN 1
    ChainsB
    EngineeredYES
    FragmentRESIDUES 203-210
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN THE LATENT MEMBRANE PROTEIN I OF EPSTEIN BARR VIRUS
    SynonymLMP-1, PROTEIN P63
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ZMS)

(-) Sites  (0, 0)

(no "Site" information available for 1ZMS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZMS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:424 -Pro A:425

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZMS)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560  1A:351-496
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560  1A:351-496
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560  3A:351-496

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003927451ENSE00001452921chr14:103243816-103244012197TRAF3_HUMAN-00--
1.2ENST000003927452ENSE00001512975chr14:103296671-103296809139TRAF3_HUMAN-00--
1.3ENST000003927453ENSE00001026101chr14:103336522-103336783262TRAF3_HUMAN1-82820--
1.4ENST000003927454ENSE00000660513chr14:103338254-10333830552TRAF3_HUMAN82-99180--
1.5ENST000003927455ENSE00000660514chr14:103341961-103342065105TRAF3_HUMAN100-134350--
1.6ENST000003927456ENSE00000660515chr14:103342695-103342862168TRAF3_HUMAN135-190560--
1.7ENST000003927457ENSE00000660516chr14:103352526-10335260681TRAF3_HUMAN191-217270--
1.8ENST000003927458ENSE00000660517chr14:103355897-10335597175TRAF3_HUMAN218-242250--
1.9ENST000003927459ENSE00000660518chr14:103357662-10335775493TRAF3_HUMAN243-273310--
1.10ENST0000039274510ENSE00000660519chr14:103363598-103363738141TRAF3_HUMAN274-320470--
1.11ENST0000039274511ENSE00000660520chr14:103369592-103369766175TRAF3_HUMAN321-379591A:313-3153
1.12ENST0000039274512ENSE00001152460chr14:103371550-1033726281079TRAF3_HUMAN379-5681901A:315-504190

(-) 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 A from PDB  Type:PROTEIN  Length:192
 aligned with TRAF3_HUMAN | Q13114 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:192
                                   386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566  
          TRAF3_HUMAN   377 NTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 568
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1zmsA00 A:313-504 Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A                                                                                                        CATH domains
               Pfam domains ---------------------------------------------MATH-1zmsA01 A:358-498                                                                                                                       ------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhh.....ee...ee......eeeeeee...hhhhh..eeeeeeeee...hhhhh.......eeeee.........eeeee...................eeeeeeeehhhhhhh......eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------MATH  PDB: A:351-496 UniProt: 415-560                                                                                                             -------- PROSITE
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.12  PDB: A:315-504 UniProt: 379-568                                                                                                                                                     Transcript 1 (2)
                 1zms A 313 NTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 504
                                   322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  

Chain B from PDB  Type:PROTEIN  Length:7
 aligned with LMP1_EBVR | P13198 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:7
            LMP1_EBVR   204 PQQATDD 210
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .ee.... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1zms B 204 PQQATDD 210

   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 1ZMS)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TRAF (11)

(-) Gene Ontology  (45, 45)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRAF3_HUMAN | Q13114)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0031996    thioesterase binding    Interacting selectively and non-covalently with any thioesterase enzyme.
    GO:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0008063    Toll signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0001817    regulation of cytokine production    Any process that modulates the frequency, rate, or extent of production of a cytokine.
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.
    GO:0032648    regulation of interferon-beta production    Any process that modulates the frequency, rate, or extent of interferon-beta production.
    GO:0030162    regulation of proteolysis    Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002224    toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    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.
cellular component
    GO:0035631    CD40 receptor complex    A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B   (LMP1_EBVR | P13198)
biological process
    GO:0039652    activation by virus of host NF-kappaB transcription factor activity    Any process in which a virus starts, promotes, or enhances the activity of the host transcription factor NF-kappaB.
    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:0039547    suppression by virus of host TRAF activity    Any process in which a virus stops, prevents, or reduces the activity of a host TRAF (tumor necrosis factor receptor-associated factor) protein. TRAFs are intracellular signal transducers that lie downstream of receptors including RIG-I, MDA-5 and Toll-like receptors (TLR) and transfer the signal to other intracellular signaling components.
    GO:0039574    suppression by virus of host TYK2 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host TYK2 (tyrosine kinase 2) activity. TYK2 is an intracellular signal-transducing tyrosine kinase that associates with the cytoplasmic tails of cytokine receptors and transmits the cytokine signal by phosphorylating receptor subunits.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0019087    transformation of host cell by virus    Any virus-induced change in the morphological, biochemical, or growth parameters of a cell.
    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: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.

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 Related Entries

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

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        TRAF3_HUMAN | Q131141flk 1fll 1kzz 1l0a 1rf3 2ecy 2gkw

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