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- PDB-8amr: Coiled-coil domain of human TRIM3 -

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Basic information

Entry
Database: PDB / ID: 8amr
TitleCoiled-coil domain of human TRIM3
ComponentsTripartite motif-containing protein 3
KeywordsANTIVIRAL PROTEIN / E3 ligase / zinc-binding / TRIM proteins / Ubiquitin
Function / homology
Function and homology information


positive regulation of toll-like receptor 3 signaling pathway / neural precursor cell proliferation / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / Interferon gamma signaling / protein polyubiquitination / ubiquitin protein ligase activity / nervous system development / protein transport / early endosome ...positive regulation of toll-like receptor 3 signaling pathway / neural precursor cell proliferation / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / Interferon gamma signaling / protein polyubiquitination / ubiquitin protein ligase activity / nervous system development / protein transport / early endosome / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 ...: / : / 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Tripartite motif-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPerez-Borrajero, C. / Murciano, B. / Hennig, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
German Research Foundation (DFG)HE 7291_1 Germany
CitationJournal: To Be Published
Title: Structural and biophysical studies of TRIM2 and TRIM3
Authors: Perez-Borrajero, C. / Hennig, J.
History
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 3
B: Tripartite motif-containing protein 3
C: Tripartite motif-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2615
Polymers104,7993
Non-polymers4632
Water1629
1
A: Tripartite motif-containing protein 3

A: Tripartite motif-containing protein 3


Theoretical massNumber of molelcules
Total (without water)69,8662
Polymers69,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
2
B: Tripartite motif-containing protein 3
C: Tripartite motif-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3284
Polymers69,8662
Non-polymers4632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.900, 167.900, 127.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and ((resid 160 through 168 and (name N...
d_2ens_1(chain "B" and ((resid 160 through 168 and (name N...
d_3ens_1(chain "C" and ((resid 160 through 168 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA10 - 105
d_12ens_1LYSLEUA109 - 152
d_21ens_1ALAALAB1 - 96
d_22ens_1LYSLEUB111 - 154
d_31ens_1ALALEUC8 - 147

NCS oper:
IDCodeMatrixVector
1given(-0.518165709656, -0.844312736366, -0.136529486002), (0.850485050972, -0.491773242713, -0.186639373723), (0.0904404522846, -0.212826410396, 0.972895391925)13.4052451551, -29.6617115112, 1.9988800113
2given(0.854462606665, 0.502995549021, 0.129958191262), (0.481508235337, -0.860694021578, 0.165395346132), (0.195047361208, -0.0787481992442, -0.97762735641)4.89116090622, -40.8257573641, 63.9629721356

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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: 34932.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM3, BERP, RNF22, RNF97 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75382
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H34O9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 4.28 Å3/Da / Density % sol: 71.25 % / Description: cubic
Crystal growTemperature: 280.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium thiocyanate, 20% (w/v) PEG 3350 / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 3.71→48.53 Å / Num. obs: 19774 / % possible obs: 99.63 % / Redundancy: 25.6 % / Biso Wilson estimate: 181.11 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1025 / Net I/σ(I): 19.26
Reflection shellResolution: 3.71→3.84 Å / Rmerge(I) obs: 2.999 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1921 / CC1/2: 0.586 / CC star: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data scaling
XDSJan 10, 2022data reduction
MxCuBEdata collection
PHENIX1.20.1_4487phasing
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model of TRIM3 coiled coil

Resolution: 3.8→48.53 Å / Cross valid method: FREE R-VALUE / Phase error: 38.4279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3213 987 5 %
Rwork0.2727 17508 -
obs0.2749 19755 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 177.59 Å2
Refinement stepCycle: LAST / Resolution: 3.8→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 19 9 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153274
X-RAY DIFFRACTIONf_angle_d0.42114431
X-RAY DIFFRACTIONf_chiral_restr0.0279543
X-RAY DIFFRACTIONf_plane_restr0.0021596
X-RAY DIFFRACTIONf_dihedral_angle_d17.2571169
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.54090063838
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.21789342295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-40.37011290.38442460X-RAY DIFFRACTION99.77
4-4.250.32851290.27912449X-RAY DIFFRACTION99.92
4.25-4.580.32011300.25252470X-RAY DIFFRACTION99.88
4.58-5.040.25761300.22312459X-RAY DIFFRACTION99.92
5.04-5.770.35081310.27562497X-RAY DIFFRACTION99.73
5.77-7.260.36591330.35692531X-RAY DIFFRACTION99.92
7.26-48.530.31061390.25172642X-RAY DIFFRACTION99.57

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