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- PDB-7o0b: TRIM3 Filamin domain -

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Basic information

Entry
Database: PDB / ID: 7o0b
TitleTRIM3 Filamin domain
ComponentsTripartite motif-containing protein 3
KeywordsRNA BINDING PROTEIN / Filamin-like domain / immunoglobulin fold
Function / homology
Function and homology information


positive regulation of toll-like receptor 3 signaling pathway / protein K63-linked ubiquitination / translation repressor activity / RING-type E3 ubiquitin transferase / protein polyubiquitination / Interferon gamma signaling / ubiquitin protein ligase activity / protein transport / nervous system development / proteasome-mediated ubiquitin-dependent protein catabolic process ...positive regulation of toll-like receptor 3 signaling pathway / protein K63-linked ubiquitination / translation repressor activity / RING-type E3 ubiquitin transferase / protein polyubiquitination / Interferon gamma signaling / ubiquitin protein ligase activity / protein transport / nervous system development / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of translation / early endosome / dendrite / Golgi apparatus / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. ...: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / 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. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsWilliams, F.P. / Yikilmazsoy, A. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1935 Germany
CitationJournal: To be published
Title: TRIM3 Filamin domain
Authors: Williams, F.P. / Yikilmazsoy, A. / Hennig, J.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: Tripartite motif-containing protein 3


Theoretical massNumber of molelcules
Total (without water)11,3131
Polymers11,3131
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.017, 33.504, 58.844
Angle α, β, γ (deg.)90.000, 117.253, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-281-

HOH

21A-284-

HOH

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Components

#1: Protein Tripartite motif-containing protein 3 / Brain-expressed RING finger protein / RING finger protein 22 / RING finger protein 97


Mass: 11312.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM3, BERP, RNF22, RNF97 / Plasmid: pETM22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75382
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Na Cacodylate pH6.5, 1M Na citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.13→28 Å / Num. obs: 5379 / % possible obs: 96.67 % / Redundancy: 3 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.2174 / Rpim(I) all: 0.1495 / Rrim(I) all: 0.265 / Net I/σ(I): 3.82
Reflection shellResolution: 2.13→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.9505 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 428 / CC1/2: 0.482 / CC star: 0.806 / Rpim(I) all: 0.6867 / Rrim(I) all: 1.178 / % possible all: 77.72

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UMG

4umg


Resolution: 2.13→28 Å / SU ML: 0.3265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 247 4.59 %
Rwork0.227 5129 -
obs0.2283 5376 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.55 Å2
Refinement stepCycle: LAST / Resolution: 2.13→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms740 0 0 111 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014749
X-RAY DIFFRACTIONf_angle_d0.4371023
X-RAY DIFFRACTIONf_chiral_restr0.0393130
X-RAY DIFFRACTIONf_plane_restr0.0023132
X-RAY DIFFRACTIONf_dihedral_angle_d29.4654113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.690.32771270.2672469X-RAY DIFFRACTION94.61
2.69-280.22781200.21092660X-RAY DIFFRACTION98.76

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