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- PDB-8a38: RING domain of human TRIM2 -

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Basic information

Entry
Database: PDB / ID: 8a38
TitleRING domain of human TRIM2
ComponentsTripartite motif-containing protein 2
KeywordsANTIVIRAL PROTEIN / RING domain / E3 ligase / zinc-binding
Function / homology
Function and homology information


regulation of neuron apoptotic process / translation repressor activity / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / Interferon gamma signaling / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of translation / zinc ion binding / cytoplasm
Similarity search - Function
NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat ...NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
Tripartite motif-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.196 Å
AuthorsPerez-Borrajero, C. / Murciano, B. / Hennig, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HE 7291_1 Germany
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
CitationJournal: To Be Published
Title: Structural and biophysical studies of TRIM2 and TRIM3
Authors: Perez-Borrajero, C. / Hennig, J.
History
DepositionJun 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif-containing protein 2
B: Tripartite motif-containing protein 2
C: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,82410
Polymers32,3663
Non-polymers4587
Water30617
1
A: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9193
Polymers10,7891
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9193
Polymers10,7891
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9854
Polymers10,7891
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.710, 48.710, 221.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 17 or (resid 18 and (name...
d_2ens_1(chain "B" and ((resid 17 and (name N or name...
d_3ens_1(chain "C" and (resid 17 or (resid 18 and (name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPCYSCYSAA17 - 6313 - 59
d_12GLNGLNLEULEUAA65 - 9061 - 86
d_21ASPASPCYSCYSBB17 - 6313 - 59
d_22GLNGLNLEULEUBB65 - 9061 - 86
d_31ASPASPCYSCYSCC17 - 6313 - 59
d_32GLNGLNLEULEUCC65 - 9061 - 86

NCS oper:
IDCodeMatrixVector
1given(0.935792781358, 0.352104213993, -0.0177339461366), (0.194258954483, -0.556955488182, -0.807504825241), (-0.294202870415, 0.752212208537, -0.589594321858)-7.55105664957, 116.618358021, 112.179857008
2given(-0.99005176981, -0.0627959452147, -0.125913312884), (0.0391606634096, -0.982503782061, 0.182078995706), (-0.13514412876, 0.175336783079, 0.975188739148)5.78092558923, 45.9084568526, -3.75348750176

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Components

#1: Protein Tripartite motif-containing protein 2 / E3 ubiquitin-protein ligase TRIM2 / RING finger protein 86 / RING-type E3 ubiquitin transferase TRIM2


Mass: 10788.639 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM2, KIAA0517, RNF86 / Plasmid: pETM41 / Details (production host): N-terminal MBP tag / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9C040, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 20% (w/v) PEG 6000, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9766 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.196→73.87 Å / Num. obs: 16478 / % possible obs: 99.8 % / Redundancy: 18.5 % / Biso Wilson estimate: 63.52 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 22.02
Reflection shellResolution: 2.196→2.275 Å / Num. unique obs: 1574 / CC1/2: 0.746 / CC star: 0.924 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSJan 10, 2022data scaling
XDSJan 10, 2022data reduction
PHENIX1.20.1_4487refinement
MxCuBEdata collection
PHENIX1.20.1_4487phasing
Coot0.9.6model building
RefinementMethod to determine structure: SAD / Resolution: 2.196→73.87 Å / SU ML: 0.4216 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.0163
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2881 1472 4.93 %
Rwork0.2582 28373 -
obs0.2592 16478 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.03 Å2
Refinement stepCycle: LAST / Resolution: 2.196→73.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 7 17 1690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311710
X-RAY DIFFRACTIONf_angle_d0.78372345
X-RAY DIFFRACTIONf_chiral_restr0.0448293
X-RAY DIFFRACTIONf_plane_restr0.0055300
X-RAY DIFFRACTIONf_dihedral_angle_d4.6782237
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.960907628155
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.907520949978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.3971340.39232568X-RAY DIFFRACTION99.7
2.27-2.350.43481360.36122598X-RAY DIFFRACTION100
2.35-2.450.351370.31952594X-RAY DIFFRACTION100
2.45-2.560.34211370.31462604X-RAY DIFFRACTION99.71
2.56-2.690.31021310.3052547X-RAY DIFFRACTION99.85
2.69-2.860.38881340.33232588X-RAY DIFFRACTION99.89
2.86-3.080.33921330.322566X-RAY DIFFRACTION100
3.08-3.390.30041340.30092573X-RAY DIFFRACTION99.93
3.39-3.880.35991270.25332571X-RAY DIFFRACTION100
3.88-4.890.25931330.22362605X-RAY DIFFRACTION100
4.89-73.870.22211360.22022559X-RAY DIFFRACTION99.34

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