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- PDB-4ghu: Crystal structure of TRAF3/Cardif -

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Basic information

Entry
Database: PDB / ID: 4ghu
TitleCrystal structure of TRAF3/Cardif
Components
  • Mitochondrial antiviral-signaling protein
  • TNF receptor-associated factor 3
KeywordsIMMUNE SYSTEM / alpha/Beta / innate immunity / IFN pathway
Function / homology
Function and homology information


DDX58/IFIH1-mediated induction of interferon-alpha/beta / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of interferon-beta production / regulation of peroxisome organization / Negative regulators of DDX58/IFIH1 signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Ovarian tumor domain proteases / TNFR2 non-canonical NF-kB pathway / PKR-mediated signaling ...DDX58/IFIH1-mediated induction of interferon-alpha/beta / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of interferon-beta production / regulation of peroxisome organization / Negative regulators of DDX58/IFIH1 signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Ovarian tumor domain proteases / TNFR2 non-canonical NF-kB pathway / PKR-mediated signaling / RIG-I signaling pathway / Toll signaling pathway / positive regulation of myeloid dendritic cell cytokine production / CD40 receptor complex / regulation of defense response to virus / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / regulation of proteolysis / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / cellular response to exogenous dsRNA / toll-like receptor 4 signaling pathway / negative regulation of NF-kappaB transcription factor activity / toll-like receptor signaling pathway / negative regulation of viral genome replication / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interferon-alpha production / positive regulation of type I interferon production / protein K63-linked ubiquitination / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / activation of innate immune response / tumor necrosis factor-mediated signaling pathway / regulation of cytokine production / positive regulation of interferon-beta production / protein tetramerization / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / peroxisome / defense response to virus / protein phosphatase binding / regulation of apoptotic process / mitochondrial outer membrane / endosome membrane / defense response to bacterium / innate immune response / ubiquitin protein ligase binding / apoptotic process / protein kinase binding / signal transduction / mitochondrion / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / IPS1, CARD domain / : / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain ...TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING 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 / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
TNF receptor-associated factor 3 / Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsZhang, P.
CitationJournal: Sci.Signal. / Year: 2012
Title: Single Amino Acid Substitutions Confer the Antiviral Activity of the TRAF3 Adaptor Protein onto TRAF5
Authors: Zhang, P. / Reichardt, A. / Liang, H. / Aliyari, R. / Cheng, D. / Wang, Y. / Xu, F. / Cheng, G. / Liu, Y.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 3
B: Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)24,9282
Polymers24,9282
Non-polymers00
Water2,720151
1
A: TNF receptor-associated factor 3
B: Mitochondrial antiviral-signaling protein

A: TNF receptor-associated factor 3
B: Mitochondrial antiviral-signaling protein

A: TNF receptor-associated factor 3
B: Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)74,7856
Polymers74,7856
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11860 Å2
ΔGint-65 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.492, 83.492, 78.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-623-

HOH

31A-633-

HOH

41A-745-

HOH

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Components

#1: Protein TNF receptor-associated factor 3 / CD40 receptor-associated factor 1 / CRAF1 / TRAFAMN


Mass: 22662.016 Da / Num. of mol.: 1 / Fragment: UNP residues 376-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Traf3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60803
#2: Protein/peptide Mitochondrial antiviral-signaling protein / Cardif / MAVS / CARD adapter inducing interferon beta / Interferon beta promoter stimulator protein ...Cardif / MAVS / CARD adapter inducing interferon beta / Interferon beta promoter stimulator protein 1 / IPS-1 / Virus-induced-signaling adapter / VISA


Mass: 2266.415 Da / Num. of mol.: 1 / Fragment: UNP residues 138-158 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VCF0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG6000, 5%(v/v) 5-methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 16376 / Num. obs: 16363 / % possible obs: 99.9 % / Observed criterion σ(F): 4.2 / Observed criterion σ(I): 16.7 / Biso Wilson estimate: 28.36 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.241100
2.24-2.281100
2.28-2.321100
2.32-2.371100
2.37-2.421100
2.42-2.481100
2.48-2.541100
2.54-2.611100
2.61-2.691100
2.69-2.771100
2.77-2.871100
2.87-2.991100
2.99-3.121100
3.12-3.291100
3.29-3.49199.9
3.76-4.141100
4.14-4.74199.9
4.74-5.97199.7
5.97-50199.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→36.819 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8538 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1542 10.07 %
Rwork0.178 --
obs0.1827 15312 93.41 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.392 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 92.93 Å2 / Biso mean: 33.468 Å2 / Biso min: 12.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.3257 Å20 Å20 Å2
2---3.3257 Å2-0 Å2
3---6.6514 Å2
Refinement stepCycle: LAST / Resolution: 2.199→36.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 0 151 1772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071693
X-RAY DIFFRACTIONf_angle_d1.0422289
X-RAY DIFFRACTIONf_chiral_restr0.069248
X-RAY DIFFRACTIONf_plane_restr0.005295
X-RAY DIFFRACTIONf_dihedral_angle_d12.846642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1994-2.27030.27551330.20221164129789
2.2703-2.35150.26621320.18641150128289
2.3515-2.44560.29251310.18571197132890
2.4456-2.55690.24251290.19281153128288
2.5569-2.69170.25791330.191205133889
2.6917-2.86020.25221350.18631224135993
2.8602-3.0810.26151390.18841257139694
3.081-3.39080.20631460.1711294144097
3.3908-3.8810.18341490.16431334148399
3.881-4.88790.17771510.15271371152299
4.8879-36.82430.23721640.19521421158599

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