[English] 日本語
Yorodumi
- PDB-3hct: Crystal structure of TRAF6 in complex with Ubc13 in the P1 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hct
TitleCrystal structure of TRAF6 in complex with Ubc13 in the P1 space group
Components
  • TNF receptor-associated factor 6
  • Ubiquitin-conjugating enzyme E2 N
KeywordsSIGNALING PROTEIN/LIGASE / cross-brace / beta-beta-alpha / Coiled coil / Cytoplasm / Metal-binding / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger / ATP-binding / DNA damage / DNA repair / Isopeptide bond / Ligase / Nucleotide-binding / SIGNALING PROTEIN-LIGASE COMPLEX
Function / homology
Function and homology information


UBC13-MMS2 complex / interleukin-17A-mediated signaling pathway / ubiquitin conjugating enzyme complex / protein kinase B binding / ubiquitin-protein transferase activator activity / CD40 signaling pathway / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway ...UBC13-MMS2 complex / interleukin-17A-mediated signaling pathway / ubiquitin conjugating enzyme complex / protein kinase B binding / ubiquitin-protein transferase activator activity / CD40 signaling pathway / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway / activation of protein kinase activity / positive regulation of protein K63-linked ubiquitination / interleukin-33-mediated signaling pathway / protein branched polyubiquitination / CD40 receptor complex / toll-like receptor 3 signaling pathway / TRIF-dependent toll-like receptor signaling pathway / DNA double-strand break processing / Regulated proteolysis of p75NTR / myeloid dendritic cell differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / regulation of immunoglobulin production / ubiquitin conjugating enzyme binding / non-canonical NF-kappaB signal transduction / DNA damage tolerance / regulation of canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / TRAF6 mediated IRF7 activation / T-helper 1 type immune response / toll-like receptor 4 signaling pathway / E2 ubiquitin-conjugating enzyme / ubiquitin-ubiquitin ligase activity / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of double-strand break repair / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cellular response to cytokine stimulus / odontogenesis of dentin-containing tooth / positive regulation of JUN kinase activity / ubiquitin conjugating enzyme activity / TRAF6 mediated NF-kB activation / positive regulation of intracellular signal transduction / autophagosome assembly / protein K63-linked ubiquitination / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / protein monoubiquitination / ubiquitin ligase complex / bone resorption / regulation of DNA repair / protein autoubiquitination / negative regulation of TORC1 signaling / positive regulation of T cell proliferation / lipid droplet / signaling adaptor activity / positive regulation of interleukin-12 production / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / antiviral innate immune response / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of interleukin-2 production / TICAM1,TRAF6-dependent induction of TAK1 complex / p75NTR recruits signalling complexes / ossification / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / NF-kB is activated and signals survival / response to interleukin-1 / NRIF signals cell death from the nucleus / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / positive regulation of protein ubiquitination / IKK complex recruitment mediated by RIP1 / tumor necrosis factor-mediated signaling pathway / PINK1-PRKN Mediated Mitophagy / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / neural tube closure / positive regulation of JNK cascade / Nonhomologous End-Joining (NHEJ) / : / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / double-strand break repair via homologous recombination / positive regulation of T cell cytokine production / G2/M DNA damage checkpoint / antigen processing and presentation of exogenous peptide antigen via MHC class II
Similarity search - Function
TNF receptor-associated factor 6, zinc finger 2 / TNF receptor-associated factor 6 zinc finger 2 / TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. ...TNF receptor-associated factor 6, zinc finger 2 / TNF receptor-associated factor 6 zinc finger 2 / TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Zinc finger, C3HC4 type (RING finger) / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsYin, Q. / Lin, S.-C. / Lamothe, B. / Lu, M. / Lo, Y.-C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. ...Yin, Q. / Lin, S.-C. / Lamothe, B. / Lu, M. / Lo, Y.-C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. / Lenardo, M.J. / Darnay, B.G. / Wu, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: E2 interaction and dimerization in the crystal structure of TRAF6.
Authors: Yin, Q. / Lin, S.C. / Lamothe, B. / Lu, M. / Lo, Y.C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. / Lenardo, M.J. / Darnay, B.G. / Wu, H.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF receptor-associated factor 6
B: Ubiquitin-conjugating enzyme E2 N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4125
Polymers31,2162
Non-polymers1963
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.985, 42.798, 49.118
Angle α, β, γ (deg.)104.610, 99.590, 108.600
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein TNF receptor-associated factor 6 / Interleukin-1 signal transducer / RING finger protein 85


Mass: 13775.906 Da / Num. of mol.: 1 / Fragment: RING and Zinc Finger 1: UNP residues 50-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF85, TRAF6 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus RIPL / References: UniProt: Q9Y4K3
#2: Protein Ubiquitin-conjugating enzyme E2 N / Ubiquitin-protein ligase N / Ubiquitin carrier protein N / Ubc13 / Bendless-like ubiquitin-conjugating enzyme


Mass: 17440.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus RIPL / References: UniProt: P61088, ubiquitin-protein ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 14, 2007 / Details: Mirrors
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.06→30 Å / Num. obs: 16146 / % possible obs: 91.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.037 / Χ2: 3.715 / Net I/σ(I): 39.692
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.06-2.131.90.06515663.16691
2.13-2.221.90.05915763.64988.8
2.22-2.321.90.05216913.43995.8
2.32-2.441.90.04716913.62995.6
2.44-2.61.90.04416793.9195.2
2.6-2.81.90.04116653.99694.9
2.8-3.081.90.03716813.9294.9
3.08-3.521.90.03216643.66294.6
3.52-4.431.90.03416163.66691.9
4.43-301.90.03413174.18974.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2GMI, 3HCS

2gmi

3hcs


Resolution: 2.1→30 Å / Occupancy max: 1.17 / Occupancy min: 0.93 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.278 1498 9.2 %
Rwork0.212 --
obs0.212 14823 90.6 %
Solvent computationBsol: 79.746 Å2
Displacement parametersBiso max: 100.66 Å2 / Biso mean: 41.53 Å2 / Biso min: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1--7.774 Å2-2.913 Å2-6.478 Å2
2---7.216 Å211.51 Å2
3---14.989 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 3 195 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5571.5
X-RAY DIFFRACTIONc_scbond_it2.2192
X-RAY DIFFRACTIONc_mcangle_it2.5332
X-RAY DIFFRACTIONc_scangle_it3.3422.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

+
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