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- PDB-4gjh: Crystal Structure of the TRAF domain of TRAF5 -

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Basic information

Entry
Database: PDB / ID: 4gjh
TitleCrystal Structure of the TRAF domain of TRAF5
ComponentsTNF receptor-associated factor 5
KeywordsIMMUNE SYSTEM / TRAF domain
Function / homology
Function and homology information


CD40 receptor complex / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / tumor necrosis factor-mediated signaling pathway / positive regulation of JNK cascade / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / positive regulation of DNA-binding transcription factor activity ...CD40 receptor complex / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / tumor necrosis factor-mediated signaling pathway / positive regulation of JNK cascade / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / positive regulation of DNA-binding transcription factor activity / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / centrosome / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / signal transduction / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
TNF receptor-associated factor 5, MATH domain / TNF receptor-associated factor 5 / TNF receptor-associated factor TRAF / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / 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 / MATH/TRAF domain ...TNF receptor-associated factor 5, MATH domain / TNF receptor-associated factor 5 / TNF receptor-associated factor TRAF / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / 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 / 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 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsZhang, P. / Reichardt, A. / Liang, H. / Wang, Y. / Cheng, D. / Aliyari, R. / Cheng, G. / Liu, Y.
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 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 5
B: TNF receptor-associated factor 5
C: TNF receptor-associated factor 5


Theoretical massNumber of molelcules
Total (without water)61,1073
Polymers61,1073
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-15 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.052, 90.579, 117.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 331:480 OR RESSEQ 483:502 )
21CHAIN B AND (RESSEQ 331:480 OR RESSEQ 483:502 )
31CHAIN C AND (RESSEQ 331:480 OR RESSEQ 485:502 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLUGLUCHAIN A AND (RESSEQ 331:480 OR RESSEQ 483:502 )AA331 - 4803 - 152
12LYSLYSASPASPCHAIN A AND (RESSEQ 331:480 OR RESSEQ 483:502 )AA483 - 502155 - 174
21HISHISGLUGLUCHAIN B AND (RESSEQ 331:480 OR RESSEQ 483:502 )BB331 - 4803 - 152
22LYSLYSASPASPCHAIN B AND (RESSEQ 331:480 OR RESSEQ 483:502 )BB483 - 502155 - 174
31HISHISGLUGLUCHAIN C AND (RESSEQ 331:480 OR RESSEQ 485:502 )CC331 - 4803 - 152
32THRTHRASPASPCHAIN C AND (RESSEQ 331:480 OR RESSEQ 485:502 )CC485 - 502157 - 174

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Components

#1: Protein TNF receptor-associated factor 5


Mass: 20369.156 Da / Num. of mol.: 3 / Fragment: UNP residues 381-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Traf5 / Production host: Escherichia coli (E. coli) / References: UniProt: P70191
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 15%(w/v) PEG10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 6, 2010
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 18987 / Num. obs: 17854 / % possible obs: 93.8 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 11.4 / Biso Wilson estimate: 44.78 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.851100
2.85-2.91100
2.9-2.961100
2.96-3.021100
3.02-3.081100
3.08-3.151100
3.15-3.231100
3.23-3.321100
3.32-3.421100
3.42-3.531100
3.53-3.65162.3
3.65-3.8172.6
3.8-3.94144.8
3.97-4.18199.9
4.18-4.441100
4.44-4.791100
4.79-5.271100
5.27-6.031100
6.03-7.591100
7.59-50198

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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: 2.805→33.073 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7707 / SU ML: 0.37 / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 909 5.13 %
Rwork0.2244 --
obs0.227 17707 92.57 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.364 Å2 / ksol: 0.277 e/Å3
Displacement parametersBiso max: 164.84 Å2 / Biso mean: 50.5671 Å2 / Biso min: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1-6.0262 Å2-0 Å20 Å2
2---19.1325 Å2-0 Å2
3---13.1063 Å2
Refinement stepCycle: LAST / Resolution: 2.805→33.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 0 39 4267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114402
X-RAY DIFFRACTIONf_angle_d1.1565813
X-RAY DIFFRACTIONf_chiral_restr0.096622
X-RAY DIFFRACTIONf_plane_restr0.004750
X-RAY DIFFRACTIONf_dihedral_angle_d15.2231605
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1355X-RAY DIFFRACTIONPOSITIONAL0.055
12B1355X-RAY DIFFRACTIONPOSITIONAL0.055
13C1336X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8046-2.98020.37051590.28462825298495
2.9802-3.21020.34051610.26729703131100
3.2102-3.53290.38781590.28392916307598
3.5329-4.04330.3441970.26111872196962
4.0433-5.09120.16591590.165130573216100
5.0912-33.07540.23491740.198531583332100

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