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- PDB-8ims: Crystal structure of TRAF7 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 8ims
TitleCrystal structure of TRAF7 coiled-coil domain
ComponentsE3 ubiquitin-protein ligase TRAF7
KeywordsSIGNALING PROTEIN / Trimer / E3 ubiquitin-protein ligase / Tumor suppressor
Function / homology
Function and homology information


protein K29-linked ubiquitination / positive regulation of ubiquitin-dependent protein catabolic process / Transferases; Acyltransferases; Aminoacyltransferases / ubiquitin ligase complex / Notch signaling pathway / regulation of ERK1 and ERK2 cascade / positive regulation of apoptotic signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process ...protein K29-linked ubiquitination / positive regulation of ubiquitin-dependent protein catabolic process / Transferases; Acyltransferases; Aminoacyltransferases / ubiquitin ligase complex / Notch signaling pathway / regulation of ERK1 and ERK2 cascade / positive regulation of apoptotic signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ribosomal large subunit assembly / cytoplasmic vesicle / positive regulation of MAPK cascade / protein ubiquitination / intracellular membrane-bounded organelle / nucleolus / apoptotic process / zinc ion binding / plasma membrane
Similarity search - Function
Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Zinc finger, RING-type, eukaryotic / RING-type zinc-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 ...Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Zinc finger, RING-type, eukaryotic / RING-type zinc-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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRAF7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHu, R. / Lin, L. / Lu, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentYG2019QNB01 China
CitationJournal: J Mol Cell Biol / Year: 2024
Title: The structure of TRAF7 coiled-coil trimer provides insight into its function in zebrafish embryonic development.
Authors: Song, X. / Hu, R. / Chen, Y. / Xiao, M. / Zhang, H. / Wu, S. / Lu, Q.
History
DepositionMar 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase TRAF7
A: E3 ubiquitin-protein ligase TRAF7
C: E3 ubiquitin-protein ligase TRAF7


Theoretical massNumber of molelcules
Total (without water)42,2873
Polymers42,2873
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.923, 169.923, 57.055
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 286 through 289 and (name N...
d_2ens_1(chain "B" and (resid 286 or (resid 287 through 289...
d_3ens_1(chain "C" and resid 286 through 376)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 286 - 376 / Label seq-ID: 28 - 118

Dom-IDAuth asym-IDLabel asym-ID
d_1AB
d_2BA
d_3CC

NCS oper:
IDCodeMatrixVector
1given(-0.512137440807, 0.089901133023, 0.854185593419), (-0.518198963654, 0.760772486145, -0.390762150665), (-0.684970857622, -0.642762017084, -0.343033400127)-127.265212753, -31.6746612529, -26.4872282446
2given(-0.515714754778, -0.512689043295, -0.686431523599), (0.0941398516893, 0.762433811802, -0.640181514061), (0.851572651057, -0.394771614364, -0.344933895789)-100.518926458, 18.4603053596, 86.8498424143

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Components

#1: Protein E3 ubiquitin-protein ligase TRAF7 / RING finger and WD repeat-containing protein 1 / RING finger protein 119 / RING-type E3 ubiquitin ...RING finger and WD repeat-containing protein 1 / RING finger protein 119 / RING-type E3 ubiquitin transferase TRAF7 / TNF receptor-associated factor 7


Mass: 14095.763 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF7, RFWD1, RNF119 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6Q0C0, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 5.62 Å3/Da / Density % sol: 78.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH6.9, 0.2M magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.3→45.09 Å / Num. obs: 14379 / % possible obs: 99.75 % / Redundancy: 4.07 % / Biso Wilson estimate: 97.36 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.22
Reflection shellResolution: 3.3→3.5 Å / Num. unique obs: 1393 / CC1/2: 0.527

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→45.09 Å / SU ML: 0.5316 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2732 761 5.29 %
Rwork0.2618 13617 -
obs0.2624 14378 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.36 Å2
Refinement stepCycle: LAST / Resolution: 3.3→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 0 9 2250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262262
X-RAY DIFFRACTIONf_angle_d0.66113016
X-RAY DIFFRACTIONf_chiral_restr0.0309334
X-RAY DIFFRACTIONf_plane_restr0.003399
X-RAY DIFFRACTIONf_dihedral_angle_d3.4344289
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS1.86470693796
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS1.85047242846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.560.38821500.34392678X-RAY DIFFRACTION99.26
3.56-3.920.29921410.30362698X-RAY DIFFRACTION99.96
3.92-4.480.28081480.2752729X-RAY DIFFRACTION99.93
4.48-5.650.27721500.26942724X-RAY DIFFRACTION100
5.65-45.090.23211720.21552788X-RAY DIFFRACTION99.83

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