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- PDB-4m4e: TRAF domain of human TRAF4 -

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Basic information

Entry
Database: PDB / ID: 4m4e
TitleTRAF domain of human TRAF4
ComponentsTNF receptor-associated factor 4
KeywordsSIGNALING PROTEIN / TRAF4 / TRAF domain / adaptor protein / regular protein
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 / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic 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: 2.6 Å
AuthorsNiu, F. / Ru, H. / Ding, W. / Ouyang, S. / Liu, Z.J.
CitationJournal: Protein Cell / Year: 2013
Title: Structural biology study of human TNF receptor associated factor 4 TRAF domain
Authors: Niu, F. / Ru, H. / Ding, W. / Ouyang, S. / Liu, Z.J.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 4
B: TNF receptor-associated factor 4
C: TNF receptor-associated factor 4


Theoretical massNumber of molelcules
Total (without water)63,2513
Polymers63,2513
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-16 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.295, 88.205, 118.425
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: 21083.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF4, CART1, MLN62, RNF83 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUZ4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2M Ammonium fluoride, 20%(w/v) Polyethylene glycol 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18582 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CA4

1ca4


Resolution: 2.6→36.031 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 1843 9.99 %RANDOM
Rwork0.2001 ---
all0.2163 19201 --
obs0.2079 18451 96.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→36.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 0 89 4096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094126
X-RAY DIFFRACTIONf_angle_d1.35584
X-RAY DIFFRACTIONf_dihedral_angle_d18.0581511
X-RAY DIFFRACTIONf_chiral_restr0.082568
X-RAY DIFFRACTIONf_plane_restr0.006730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.594-2.66430.32971340.2385120594
2.6643-2.74270.34561440.2414130199
2.7427-2.83110.34881440.2259130799
2.8311-2.93230.29831430.2253128199
2.9323-3.04960.30631440.2477130199
3.0496-3.18830.32851470.22391318100
3.1883-3.35630.30841440.21331308100
3.3563-3.56640.31531450.21261306100
3.5664-3.84150.2828970.21785764
3.8415-4.22760.28771430.1783129397
4.2276-4.83810.20511490.16191338100
4.8381-6.09070.24661510.1705136199
6.0907-36.03470.23631580.1987143299

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