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- PDB-4k8u: Crystal structure of TRAF4 TRAF domain -

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Basic information

Entry
Database: PDB / ID: 4k8u
TitleCrystal structure of TRAF4 TRAF domain
ComponentsTNF receptor-associated factor 4
KeywordsSIGNALING PROTEIN / TRAF domain / TRAF fold / Protein interaction / signaling molecule binding
Function / homology
Function and homology information


respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / bicellular tight junction / positive regulation of protein kinase activity / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase ...respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / bicellular tight junction / positive regulation of protein kinase activity / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / fibrillar center / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / cytoskeleton / innate immune response / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 4, MATH 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 / MATH/TRAF domain ...TNF receptor-associated factor 4, MATH 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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
TNF receptor-associated factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsPark, H.H. / Yoon, J.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the TRAF4 TRAF domain with a coiled-coil domain and its implications for the TRAF4 signalling pathway.
Authors: Yoon, J.H. / Cho, Y.J. / Park, H.H.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Data collection
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 4
B: TNF receptor-associated factor 4
C: TNF receptor-associated factor 4


Theoretical massNumber of molelcules
Total (without water)68,4933
Polymers68,4933
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.949, 87.989, 117.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TNF receptor-associated factor 4 / Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene ...Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene 62 protein / MLN 62 / RING finger protein 83


Mass: 22830.863 Da / Num. of mol.: 3 / Fragment: UNP residues 281-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUZ4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEG 3350, 0.14M Magnessium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→42 Å / Num. obs: 27677 / Observed criterion σ(F): 3 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.4 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→41.589 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7417 / SU ML: 0.67 / σ(F): 0.04 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 1383 5.03 %Random
Rwork0.2374 ---
obs0.2397 27521 99.22 %-
all-28354 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.454 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 126.36 Å2 / Biso mean: 61.629 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.698 Å20 Å20 Å2
2--0.96 Å2-0 Å2
3----0.262 Å2
Refinement stepCycle: LAST / Resolution: 2.302→41.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 0 46 4340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014414
X-RAY DIFFRACTIONf_angle_d1.4515972
X-RAY DIFFRACTIONf_chiral_restr0.116610
X-RAY DIFFRACTIONf_plane_restr0.006780
X-RAY DIFFRACTIONf_dihedral_angle_d17.4321637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3022-2.38450.40741170.32552513263097
2.3845-2.480.4151260.31272594272099
2.48-2.59280.37441270.304825822709100
2.5928-2.72950.38361390.313126062745100
2.7295-2.90050.34141600.276325562716100
2.9005-3.12440.28591380.272326282766100
3.1244-3.43860.30151350.248226222757100
3.4386-3.93590.28471450.221126342779100
3.9359-4.95750.22341390.19192660279999
4.9575-41.59530.24571570.2192743290098

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