[English] 日本語
Yorodumi
- PDB-8amr: Coiled-coil domain of human TRIM3 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / early endosome / negative regulation of translation / 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. / Filamin/ABP280 repeat-like ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
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 / Polyethylene glycol


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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more