[English] 日本語
Yorodumi
- PDB-3m06: Crystal Structure of TRAF2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m06
TitleCrystal Structure of TRAF2
ComponentsTNF receptor-associated factor 2TRAF2
KeywordsPROTEIN BINDING / TNF RECEPTOR ASSOCIATED factor / acetylation / alternative splicing / apoptosis / coiled coil / cytoplasm / metal-binding / Ubl conjugation
Function / homology
Function and homology information


CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / Defective RIPK1-mediated regulated necrosis / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / tumor necrosis factor binding / Regulation by c-FLIP / CASP8 activity is inhibited ...CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / Defective RIPK1-mediated regulated necrosis / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / tumor necrosis factor binding / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / 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 / mRNA stabilization / positive regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / tumor necrosis factor receptor binding / regulation of immunoglobulin production / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / non-canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / TRAF6 mediated NF-kB activation / regulation of JNK cascade / regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / protein autoubiquitination / ubiquitin ligase complex / signaling adaptor activity / 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 / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / positive regulation of T cell cytokine production / ubiquitin-protein transferase activity / positive regulation of DNA-binding transcription factor activity / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / protein-containing complex assembly / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / molecular adaptor activity / Ub-specific processing proteases / membrane raft / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
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. ...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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsKabaleeswaran, V. / Wu, H.
CitationJournal: Mol.Cell / Year: 2010
Title: Crystal structures of the TRAF2: cIAP2 and the TRAF1: TRAF2: cIAP2 complexes: affinity, specificity, and regulation.
Authors: Zheng, C. / Kabaleeswaran, V. / Wang, Y. / Cheng, G. / Wu, H.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF receptor-associated factor 2
B: TNF receptor-associated factor 2
C: TNF receptor-associated factor 2
D: TNF receptor-associated factor 2
E: TNF receptor-associated factor 2
F: TNF receptor-associated factor 2


Theoretical massNumber of molelcules
Total (without water)50,4096
Polymers50,4096
Non-polymers00
Water1,09961
1
A: TNF receptor-associated factor 2
B: TNF receptor-associated factor 2
C: TNF receptor-associated factor 2


Theoretical massNumber of molelcules
Total (without water)25,2043
Polymers25,2043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-74 kcal/mol
Surface area10580 Å2
MethodPISA
2
D: TNF receptor-associated factor 2
E: TNF receptor-associated factor 2
F: TNF receptor-associated factor 2


Theoretical massNumber of molelcules
Total (without water)25,2043
Polymers25,2043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-78 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.706, 150.706, 86.728
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
TNF receptor-associated factor 2 / TRAF2 / Tumor necrosis factor type 2 receptor-associated protein 3


Mass: 8401.493 Da / Num. of mol.: 6 / Fragment: Residues 266-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF2 / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q12933
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 70.54 % / Mosaicity: 0.347 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% PEG3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11K, H, -L20.475
ReflectionResolution: 2.64→50 Å / Num. obs: 20824 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.053 / Χ2: 1.092 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.64-2.695.10.3765150.96845.5
2.69-2.745.70.34911191.004100
2.74-2.85.80.28111351.046100
2.8-2.865.80.23711441.079100
2.86-2.935.70.20410991.137100
2.93-35.80.1811461.212100
3-3.085.80.1511311.259100
3.08-3.175.80.14411161.176100
3.17-3.285.80.12811491.198100
3.28-3.395.80.111311.151100
3.39-3.535.80.0911251.112100
3.53-3.695.80.08611121.154100
3.69-3.885.80.07811371.138100
3.88-4.135.80.06711280.91100
4.13-4.455.80.06511280.922100
4.45-4.895.80.06511200.951100
4.89-5.65.80.06311401.195100
5.6-7.055.70.06411251.003100
7.05-505.80.0411241.06399.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M0A

3m0a


Resolution: 2.67→36.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.067 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1053 5.1 %RANDOM
Rwork0.192 19768 --
obs0.194 20821 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.46 Å2
Baniso -1Baniso -2Baniso -3
1--12.73 Å20 Å20 Å2
2---12.73 Å20 Å2
3---25.11 Å2
Refinement stepCycle: LAST / Resolution: 2.67→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 0 61 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212637
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9693579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.11824.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.2915431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3841519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021912
X-RAY DIFFRACTIONr_mcbond_it0.661.51860
X-RAY DIFFRACTIONr_mcangle_it1.42822917
X-RAY DIFFRACTIONr_scbond_it2.5173777
X-RAY DIFFRACTIONr_scangle_it4.4034.5662
LS refinement shellResolution: 2.67→2.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 62 -
Rwork0.282 1436 -
all-1498 -
obs--97.02 %

+
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://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