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- PDB-4z8m: Crystal structure of the MAVS-TRAF6 complex -

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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 6TRAF6
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 / tumor necrosis factor receptor superfamily binding / protein kinase B binding / interleukin-17A-mediated signaling pathway / MyD88 dependent cascade initiated on endosome / positive regulation of chemokine (C-C motif) ligand 5 production / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / tumor necrosis factor receptor superfamily binding / protein kinase B binding / interleukin-17A-mediated signaling pathway / MyD88 dependent cascade initiated on endosome / positive regulation of chemokine (C-C motif) ligand 5 production / 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 / positive regulation of myeloid dendritic cell cytokine production / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex / positive regulation of lipopolysaccharide-mediated signaling pathway / CARD domain binding / myeloid dendritic cell differentiation / TRIF-dependent toll-like receptor signaling pathway / Regulated proteolysis of p75NTR / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / activation of NF-kappaB-inducing kinase activity / positive regulation of transcription regulatory region DNA binding / positive regulation of response to cytokine stimulus / positive regulation of osteoclast differentiation / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / ubiquitin conjugating enzyme binding / regulation of immunoglobulin production / peroxisomal membrane / regulation of canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / T-helper 1 type immune response / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / activation of protein kinase activity / odontogenesis of dentin-containing tooth / non-canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / cellular response to cytokine stimulus / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / autophagosome assembly / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / protein autoubiquitination / ubiquitin ligase complex / signaling adaptor activity / positive regulation of JUN kinase activity / bone resorption / lipopolysaccharide-mediated signaling pathway / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / positive regulation of defense response to virus by host / 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 T cell proliferation / TICAM1,TRAF6-dependent induction of TAK1 complex / tumor necrosis factor-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-2 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / activation of innate immune response / NRIF signals cell death from the nucleus / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / NF-kB is activated and signals survival / molecular condensate scaffold activity / lipid droplet / response to interleukin-1 / ossification / TICAM1, RIP1-mediated IKK complex recruitment / osteoclast differentiation / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / Regulation of NF-kappa B signaling / neural tube closure / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / mitochondrial membrane / TAK1-dependent IKK and NF-kappa-B activation
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 / 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 / IPS1, CARD 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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Components

#1: Protein TNF receptor-associated factor 6 / TRAF6 / 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

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Experimental details

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Experiment

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

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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

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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

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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

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