[English] 日本語
Yorodumi
- PDB-1czy: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1czy
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN TRAF2 AND AN LMP1 BINDING PEPTIDE
Components
  • LATENT MEMBRANE PROTEIN 1
  • TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
KeywordsAPOPTOSIS / BETA SANDWICH / PROTEIN-PEPTIDE COMPLEX / SIGNALING PROTEIN
Function / homology
Function and homology information


: / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP ...: / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / programmed necrotic cell death / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / signal transduction involved in regulation of gene expression / activation of NF-kappaB-inducing kinase activity / vesicle membrane / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / mRNA stabilization / thioesterase binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / transformation of host cell by virus / non-canonical NF-kappaB signal transduction / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / regulation of JNK cascade / host cell membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / regulation of protein-containing complex assembly / protein autoubiquitination / signaling adaptor activity / ubiquitin ligase complex / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / protein catabolic process / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / positive regulation of DNA-binding transcription factor activity / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / protein-containing complex assembly / regulation of apoptotic process / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / membrane => GO:0016020 / molecular adaptor activity / Ub-specific processing proteases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / host cell plasma membrane / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Herpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa ...Herpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Latent membrane protein 1 / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsYe, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H.
Citation
Journal: Mol.Cell / Year: 1999
Title: The structural basis for the recognition of diverse receptor sequences by TRAF2.
Authors: Ye, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H.
#1: Journal: Nature / Year: 1999
Title: Structural Basis for Self-Association and Receptor Recognition of Human Traf2
Authors: Park, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H.
History
DepositionSep 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
C: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
D: LATENT MEMBRANE PROTEIN 1
E: LATENT MEMBRANE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)58,6985
Polymers58,6985
Non-polymers00
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-29 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.200, 76.800, 66.900
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 / TRAF2


Mass: 19032.953 Da / Num. of mol.: 3 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24D / Production host: Escherichia coli (E. coli) / References: UniProt: Q12933
#2: Protein/peptide LATENT MEMBRANE PROTEIN 1 / LMP1


Mass: 799.783 Da / Num. of mol.: 2 / Fragment: TRAF2-BINDING REGION / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS)
References: UniProt: P03230
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 3 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH ...THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 3 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH DOES NOT HAVE THE PEPTIDE BOUND DUE TO CONFLICT WITH CRYSTAL PACKING.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: PEG4K, MES BUFFER, pH 6.00, VAPOR DIFFUSION, temperature 20K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-15 %PEG400011
20.1 MMES11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.018
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.15

-
Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2→20 Å
RfactorSelection details
Rfree0.245 6%
Rwork0.206 -
obs0.206 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 0 391 4348

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more