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- PDB-3zjb: The structure of the TRAF domain of human TRAF4 -

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Basic information

Entry
Database: PDB / ID: 3zjb
TitleThe structure of the TRAF domain of human TRAF4
ComponentsTNF RECEPTOR-ASSOCIATED FACTOR 4
KeywordsSIGNALING 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: 1.84 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Rousseau, A. / Rogna, D. / Nomine, Y. / Rio, M.-C. / Tomasetto, C. / Alpy, F.
CitationJournal: Plos Biol. / Year: 2013
Title: Traf4 is a Novel Phosphoinositide-Binding Protein Modulating Tight Junctions and Favoring Cell Migration.
Authors: Rousseau, A. / Mcewen, A.G. / Poussin-Courmontagne, P. / Rognan, D. / Nomine, Y. / Rio, M.-C. / Tomasetto, C. / Alpy, F.
History
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2906
Polymers68,1833
Non-polymers1063
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-56.7 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.620, 85.440, 61.650
Angle α, β, γ (deg.)90.00, 108.08, 90.00
Int Tables number4
Space group name H-MP1211

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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: 22727.721 Da / Num. of mol.: 3 / Fragment: MATH DOMAIN, RESIDUES 283-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BUZ4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.02 Å3/Da / Density % sol: 39.2 % / Description: NONE
Crystal growpH: 7 / Details: 15% PEG 4000, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2011 / Details: MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.85→58.6 Å / Num. obs: 46352 / % possible obs: 97.3 % / Observed criterion σ(I): 6 / Redundancy: 3.6 % / Biso Wilson estimate: 26.83 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 1.04 / % possible all: 73.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA9

1ca9


Resolution: 1.84→58.6 Å / Cor.coef. Fo:Fc: 0.9615 / Cor.coef. Fo:Fc free: 0.9421 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 2292 5.08 %RANDOM
Rwork0.1632 ---
obs0.165 45095 96.46 %-
Displacement parametersBiso mean: 33.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.4548 Å20 Å2-1.1439 Å2
2---0.5772 Å20 Å2
3---1.032 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 1.84→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 3 575 4863
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046062HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1579SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes666HARMONIC5
X-RAY DIFFRACTIONt_it4478HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion16.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion532SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5341SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2755 118 5.11 %
Rwork0.2558 2193 -
all0.2568 2311 -
obs--96.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5954-0.2849-0.0431.0506-0.09251.27740.05940.0420.0146-0.1458-0.02090.08460.0236-0.006-0.0384-0.0230.0066-0.007-0.067-0.0003-0.0336-3.7415-30.311460.3273
20.7426-0.019-0.04460.9729-0.3821.40720.05580.061-0.0244-0.04750.00150.02580.0341-0.0765-0.0573-0.0665-0.0011-0.0018-0.03890.0102-0.0621-10.7127-1.975844.6079
30.7044-0.2138-0.1491.17490.02231.29170.0524-0.00710.00380.00840.0093-0.0074-0.1-0.0205-0.0618-0.0450.0020.002-0.0354-0.0066-0.0686-7.8019-1.757377.457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|285 - A|464}
2X-RAY DIFFRACTION2{B|286 - B|471}
3X-RAY DIFFRACTION3{C|287 - C|464}

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