[English] 日本語
Yorodumi
- PDB-4z8m: Crystal structure of the MAVS-TRAF6 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z8m
TitleCrystal structure of the MAVS-TRAF6 complex
Components
  • Peptide from Mitochondrial antiviral-signaling protein
  • TNF receptor-associated factor 6
KeywordsLIGASE/SIGNALING PROTEIN / Complex / Adaptor / E3 ligase / Antiviral signaling / LIGASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / protein kinase B binding / interleukin-17A-mediated signaling pathway / positive regulation of transcription regulatory region DNA binding / CD40 signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / MyD88 dependent cascade initiated on endosome / interleukin-17-mediated signaling pathway ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / protein kinase B binding / interleukin-17A-mediated signaling pathway / positive regulation of transcription regulatory region DNA binding / CD40 signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / MyD88 dependent cascade initiated on endosome / interleukin-17-mediated signaling pathway / positive regulation of myeloid dendritic cell cytokine production / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / protein branched polyubiquitination / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex / CARD domain binding / TRIF-dependent toll-like receptor signaling pathway / myeloid dendritic cell differentiation / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Regulated proteolysis of p75NTR / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / positive regulation of osteoclast differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / regulation of immunoglobulin production / ubiquitin conjugating enzyme binding / activation of protein kinase activity / extrinsic component of cytoplasmic side of plasma membrane / regulation of canonical NF-kappaB signal transduction / non-canonical NF-kappaB signal transduction / peroxisomal membrane / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / TRAF6 mediated IRF7 activation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / negative regulation of type I interferon-mediated signaling pathway / T-helper 1 type immune response / ubiquitin-ubiquitin ligase activity / type I interferon-mediated signaling pathway / negative regulation of viral genome replication / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / cellular response to exogenous dsRNA / cellular response to cytokine stimulus / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / odontogenesis of dentin-containing tooth / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / positive regulation of JUN kinase activity / autophagosome assembly / protein K63-linked ubiquitination / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / ubiquitin ligase complex / bone resorption / positive regulation of T cell proliferation / protein autoubiquitination / signaling adaptor activity / positive regulation of defense response to virus by host / lipid droplet / antiviral innate immune response / positive regulation of interleukin-12 production / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / 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 / TICAM1,TRAF6-dependent induction of TAK1 complex / positive regulation of interleukin-2 production / response to interleukin-1 / p75NTR recruits signalling complexes / activation of innate immune response / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / osteoclast differentiation / NF-kB is activated and signals survival / ossification / positive regulation of interferon-beta production / NRIF signals cell death from the nucleus / lipopolysaccharide-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-8 production / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / neural tube closure / molecular condensate scaffold activity / mitochondrial membrane
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 / IPS1, CARD domain / : / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain ...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 / IPS1, CARD domain / : / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Zinc finger, C3HC4 type (RING finger) / Caspase recruitment domain / Caspase recruitment domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mitochondrial antiviral-signaling protein / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsShi, Z.B. / Zhou, Z.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Insights into Mitochondrial Antiviral Signaling Protein (MAVS)-Tumor Necrosis Factor Receptor-associated Factor 6 (TRAF6) Signaling
Authors: Shi, Z. / Zhang, Z. / Zhang, Z. / Wang, Y. / Li, C. / Wang, X. / He, F. / Sun, L. / Jiao, S. / Shi, W. / Zhou, Z.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF receptor-associated factor 6
B: TNF receptor-associated factor 6
C: Peptide from Mitochondrial antiviral-signaling protein
D: Peptide from Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)43,6644
Polymers43,6644
Non-polymers00
Water00
1
A: TNF receptor-associated factor 6
C: Peptide from Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)21,8322
Polymers21,8322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area8320 Å2
MethodPISA
2
B: TNF receptor-associated factor 6
D: Peptide from Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)21,8322
Polymers21,8322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.392, 78.035, 108.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein TNF receptor-associated factor 6 / E3 ubiquitin-protein ligase TRAF6 / Interleukin-1 signal transducer / RING finger protein 85


Mass: 19778.783 Da / Num. of mol.: 2 / Fragment: UNP residues 346-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6, RNF85 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Condonplus
References: UniProt: Q9Y4K3, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Peptide from Mitochondrial antiviral-signaling protein / MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein ...MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein 1 / IPS-1 / Putative NF-kappa-B-activating protein 031N / Virus-induced-signaling adapter / VISA


Mass: 2053.167 Da / Num. of mol.: 2 / Fragment: UNP residues 450-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Condonplus / References: UniProt: Q7Z434

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% (v/v) Tacsimate pH 6.0, 0.1 M MES pH 6.0, and 25% (w/v) polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 31, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 9814 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 18.9
Reflection shellResolution: 2.95→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LB4

1lb4


Resolution: 2.95→43.498 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 975 10 %Random selection
Rwork0.1865 ---
obs0.1919 9747 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→43.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 0 0 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012608
X-RAY DIFFRACTIONf_angle_d1.2953549
X-RAY DIFFRACTIONf_dihedral_angle_d14.491932
X-RAY DIFFRACTIONf_chiral_restr0.047386
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.10550.35651380.25961243X-RAY DIFFRACTION100
3.1055-3.30.31821370.21971232X-RAY DIFFRACTION100
3.3-3.55470.241390.18941244X-RAY DIFFRACTION100
3.5547-3.91220.21311380.17711253X-RAY DIFFRACTION100
3.9122-4.47780.20671410.15371258X-RAY DIFFRACTION99
4.4778-5.63960.21051390.15921252X-RAY DIFFRACTION98
5.6396-43.50240.2411430.21131290X-RAY DIFFRACTION95

+
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