[English] 日本語
Yorodumi
- PDB-4nqj: Structure of coiled-coil domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nqj
TitleStructure of coiled-coil domain
ComponentsE3 ubiquitin-protein ligase TRIM69
KeywordsLIGASE / coiled-coil domain / oligomerization
Function / homology
Function and homology information


RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / nuclear speck / apoptotic process / identical protein binding / metal ion binding / nucleus ...RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / nuclear speck / apoptotic process / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily ...zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM69
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.152 Å
AuthorsYang, M. / Li, Y.
CitationJournal: Cell Res. / Year: 2014
Title: Structural insights into the TRIM family of ubiquitin E3 ligases.
Authors: Li, Y. / Wu, H. / Wu, W. / Zhuo, W. / Liu, W. / Zhang, Y. / Cheng, M. / Chen, Y.G. / Gao, N. / Yu, H. / Wang, L. / Li, W. / Yang, M.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM69
B: E3 ubiquitin-protein ligase TRIM69
C: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0228
Polymers62,4693
Non-polymers2,5535
Water3,531196
1
A: E3 ubiquitin-protein ligase TRIM69
B: E3 ubiquitin-protein ligase TRIM69
C: E3 ubiquitin-protein ligase TRIM69
hetero molecules

A: E3 ubiquitin-protein ligase TRIM69
B: E3 ubiquitin-protein ligase TRIM69
C: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,04416
Polymers124,9386
Non-polymers5,10610
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area42660 Å2
ΔGint-341 kcal/mol
Surface area59870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.097, 101.064, 233.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein E3 ubiquitin-protein ligase TRIM69 / RFP-like domain-containing protein trimless / RING finger protein 36 / Tripartite motif-containing protein 69


Mass: 20822.973 Da / Num. of mol.: 3 / Fragment: UNP residues 143-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM69 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86WT6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUESE IS NATURAL VARIANT, RS3100139

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 6, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 52974 / Num. obs: 52974 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35 / Biso Wilson estimate: 40.67 Å2
Reflection shellHighest resolution: 2.15 Å / % possible all: 98.72

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: SAD

Resolution: 2.152→39.139 Å / FOM work R set: 0.7787 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2691 5.08 %
Rwork0.2162 50284 -
obs0.2179 52974 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.84 Å2 / Biso mean: 64.82 Å2 / Biso min: 33.43 Å2
Refinement stepCycle: LAST / Resolution: 2.152→39.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 175 196 4697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084585
X-RAY DIFFRACTIONf_angle_d1.0386142
X-RAY DIFFRACTIONf_chiral_restr0.063720
X-RAY DIFFRACTIONf_plane_restr0.004760
X-RAY DIFFRACTIONf_dihedral_angle_d18.041777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1516-2.19070.27291180.26182420253890
2.1907-2.23280.2751380.24862481261995
2.2328-2.27840.33041520.2572597274998
2.2784-2.32790.26681270.25072645277299
2.3279-2.38210.331360.245326222758100
2.3821-2.44160.29281600.231726452805100
2.4416-2.50760.24671340.224126592793100
2.5076-2.58140.27341490.22926322781100
2.5814-2.66470.29561400.23272652279299
2.6647-2.75990.31021340.224326572791100
2.7599-2.87040.26691490.229626712820100
2.8704-3.0010.27091470.235426482795100
3.001-3.15910.24311490.244426642813100
3.1591-3.3570.26931390.233726862825100
3.357-3.6160.25191370.210627142851100
3.616-3.97960.24221460.195126792825100
3.9796-4.55470.21210.183927312852100
4.5547-5.73550.22261590.194327312890100
5.7355-39.14540.24031560.22172750290696
Refinement TLS params.Method: refined / Origin x: -4.9701 Å / Origin y: -23.4267 Å / Origin z: 49.2064 Å
111213212223313233
T0.4749 Å2-0.007 Å20.1551 Å2-0.3752 Å20.0059 Å2--0.4698 Å2
L0.0836 °20.1032 °2-0.0196 °2--0.1159 °2-0.1361 °2--0.1515 °2
S-0.0255 Å °0.0902 Å °-0.0203 Å °0.0466 Å °0.0003 Å °-0.0029 Å °-0.0327 Å °-0.0671 Å °0.0221 Å °
Refinement TLS groupSelection details: ALL

+
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