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- PDB-5e1t: Crystal structure of TRAF1 TRAF domain -

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Basic information

Entry
Database: PDB / ID: 5e1t
TitleCrystal structure of TRAF1 TRAF domain
ComponentsTNF receptor-associated factor 1
KeywordsPROTEIN BINDING / Protein interaction domain
Function / homology
Function and homology information


regulation of extrinsic apoptotic signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / positive regulation of NF-kappaB transcription factor activity ...regulation of extrinsic apoptotic signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / apoptotic process / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 1, MATH domain / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TNF receptor-associated factor TRAF, metazoa / : / 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. ...TNF receptor-associated factor 1, MATH domain / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TNF receptor-associated factor TRAF, metazoa / : / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
TNF receptor-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsPark, H.H. / Kim, C.M.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of TRAF1 TRAF domain and its implications in the TRAF1-mediated intracellular signaling pathway
Authors: Kim, C.M. / Choi, J.Y. / Bhat, E.A. / Jeong, J.H. / Son, Y.J. / Kim, S. / Park, H.H.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 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 1
B: TNF receptor-associated factor 1
C: TNF receptor-associated factor 1


Theoretical massNumber of molelcules
Total (without water)67,9383
Polymers67,9383
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-51 kcal/mol
Surface area29090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.352, 79.404, 108.982
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 1 / TRAF protein / Epstein-Barr virus-induced protein 6


Mass: 22645.951 Da / Num. of mol.: 3 / Fragment: UNP residues 220-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF1, EBI6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13077
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: (NH4)2SO4, NaCl / PH range: 9.0-9.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15860 / % possible obs: 94.7 % / Redundancy: 5 % / Biso Wilson estimate: 58.57 Å2 / Rsym value: 0.06 / Net I/σ(I): 31.2
Reflection shellHighest resolution: 2.8 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 729 / Rsym value: 0.19 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.8→29.523 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1298 8.22 %
Rwork0.2107 --
obs0.2149 15792 94.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 0 13 4612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114696
X-RAY DIFFRACTIONf_angle_d1.4426335
X-RAY DIFFRACTIONf_dihedral_angle_d17.0182853
X-RAY DIFFRACTIONf_chiral_restr0.069700
X-RAY DIFFRACTIONf_plane_restr0.009812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.91230.29171290.27061534X-RAY DIFFRACTION92
2.9123-3.04470.29871350.24661541X-RAY DIFFRACTION92
3.0447-3.2050.27511370.23491583X-RAY DIFFRACTION95
3.205-3.40560.27561430.23161597X-RAY DIFFRACTION96
3.4056-3.66810.33461460.2091624X-RAY DIFFRACTION97
3.6681-4.03640.25541510.21311646X-RAY DIFFRACTION97
4.0364-4.61850.23891450.17781633X-RAY DIFFRACTION96
4.6185-5.81160.23651550.18791667X-RAY DIFFRACTION97
5.8116-29.52440.2491570.21771669X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 13.9021 Å / Origin y: -17.6562 Å / Origin z: -27.6917 Å
111213212223313233
T0.3184 Å2-0.0037 Å20.0366 Å2-0.3239 Å20.0251 Å2--0.3068 Å2
L0.6515 °2-0.2526 °20.0416 °2-0.5667 °2-0.1998 °2--0.4244 °2
S0.0073 Å °0.0024 Å °0.0516 Å °0.0679 Å °0.0598 Å °0.0387 Å °0.0032 Å °-0.1397 Å °0.0007 Å °
Refinement TLS groupSelection details: all

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