[English] 日本語
Yorodumi
- PDB-7w0s: TRIM7 in complex with C-terminal peptide of 2C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w0s
TitleTRIM7 in complex with C-terminal peptide of 2C
Components
  • E3 ubiquitin-protein ligase TRIM7
  • peptide
KeywordsANTIVIRAL PROTEIN
Function / homology
Function and homology information


antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / innate immune response / Golgi apparatus / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / SPRY domain / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger ...zinc finger of C3HC4-type, RING / SPRY domain / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, H. / Liang, X. / Li, X.Z.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.
Authors: Liang, X. / Xiao, J. / Li, X. / Liu, Y. / Lu, Y. / Wen, Y. / Li, Z. / Che, X. / Ma, Y. / Zhang, X. / Zhang, Y. / Jian, D. / Wang, P. / Xuan, C. / Yu, G. / Li, L. / Zhang, H.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: 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
B: E3 ubiquitin-protein ligase TRIM7
A: peptide
C: E3 ubiquitin-protein ligase TRIM7
D: peptide
E: E3 ubiquitin-protein ligase TRIM7
F: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27319
Polymers62,3036
Non-polymers97113
Water12,106672
1
B: E3 ubiquitin-protein ligase TRIM7
A: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9845
Polymers20,7682
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint1 kcal/mol
Surface area8430 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase TRIM7
D: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1227
Polymers20,7682
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-0 kcal/mol
Surface area8400 Å2
MethodPISA
3
E: E3 ubiquitin-protein ligase TRIM7
F: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1687
Polymers20,7682
Non-polymers4005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-3 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.131, 53.479, 80.873
Angle α, β, γ (deg.)90.000, 118.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules BCEADF

#1: Protein E3 ubiquitin-protein ligase TRIM7 / Glycogenin-interacting protein / RING finger protein 90 / Tripartite motif-containing protein 7


Mass: 19689.295 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C029, RING-type E3 ubiquitin transferase
#2: Protein/peptide peptide


Mass: 1078.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus

-
Non-polymers , 4 types, 685 molecules

#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion / Details: PEG 3350, potassium nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→42.68 Å / Num. obs: 107169 / % possible obs: 91.58 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.89
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 6515 / CC1/2: 0.902

-
Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6uma

6uma


Resolution: 1.4→42.34 Å / SU ML: 0.1189 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.7155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1685 5112 4.77 %
Rwork0.1512 102047 -
obs0.152 107159 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.12 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 63 672 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944311
X-RAY DIFFRACTIONf_angle_d1.08725846
X-RAY DIFFRACTIONf_chiral_restr0.0869624
X-RAY DIFFRACTIONf_plane_restr0.0111765
X-RAY DIFFRACTIONf_dihedral_angle_d7.8586592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.410.2057680.2291861X-RAY DIFFRACTION49.4
1.41-1.430.2734790.20312065X-RAY DIFFRACTION54.93
1.43-1.450.219980.19492289X-RAY DIFFRACTION60.92
1.45-1.470.21461210.18332504X-RAY DIFFRACTION68.45
1.47-1.480.20381270.17962689X-RAY DIFFRACTION72.76
1.48-1.510.19751730.17752954X-RAY DIFFRACTION80.49
1.51-1.530.2041620.17133203X-RAY DIFFRACTION85.69
1.53-1.550.18251540.16633351X-RAY DIFFRACTION90.66
1.55-1.570.19181690.16423490X-RAY DIFFRACTION94.23
1.57-1.60.17131820.16973662X-RAY DIFFRACTION98.44
1.6-1.630.19262050.16763666X-RAY DIFFRACTION99.56
1.63-1.660.19261930.18563676X-RAY DIFFRACTION99.15
1.66-1.690.20052420.18063615X-RAY DIFFRACTION99.02
1.69-1.720.18312330.16813656X-RAY DIFFRACTION99.34
1.72-1.760.19312130.16623649X-RAY DIFFRACTION99.28
1.76-1.80.17941640.15863708X-RAY DIFFRACTION98.62
1.8-1.850.16592100.14653625X-RAY DIFFRACTION98.54
1.85-1.90.15781920.14293674X-RAY DIFFRACTION99.54
1.9-1.950.16541410.14113722X-RAY DIFFRACTION99.38
1.95-2.020.15752160.14513666X-RAY DIFFRACTION99.41
2.02-2.090.1741770.1433709X-RAY DIFFRACTION99.11
2.09-2.170.15812130.13823657X-RAY DIFFRACTION98.98
2.17-2.270.15911830.13753690X-RAY DIFFRACTION98.9
2.27-2.390.17231090.13683794X-RAY DIFFRACTION99.46
2.39-2.540.16451950.14093723X-RAY DIFFRACTION99.64
2.54-2.730.16131830.14583692X-RAY DIFFRACTION98.83
2.74-3.010.17241780.14723711X-RAY DIFFRACTION98.73
3.01-3.450.15572120.14233724X-RAY DIFFRACTION99.57
3.45-4.340.13752010.1373715X-RAY DIFFRACTION98.69
4.34-42.340.19531190.17033907X-RAY DIFFRACTION98.97
Refinement TLS params.Method: refined / Origin x: 6.77917058983 Å / Origin y: -16.8107987031 Å / Origin z: 20.2705303866 Å
111213212223313233
T0.118420026458 Å20.00772141227143 Å20.000275178130204 Å2-0.0953910124642 Å2-0.00250439094405 Å2--0.113287598775 Å2
L0.195512177504 °20.0271464044481 °2-0.0321949421508 °2-0.0939847785896 °2-0.0407526765126 °2--0.183435129263 °2
S-0.0142789572141 Å °0.0272106084141 Å °-0.00271459212043 Å °0.00442115464971 Å °0.0125027129903 Å °-0.00980199697408 Å °-0.012137509187 Å °0.00141782632471 Å °-0.000449398977722 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