[English] 日本語
Yorodumi
- PDB-7yc2: Crystal structure of auxiliary protein in complex with human protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yc2
TitleCrystal structure of auxiliary protein in complex with human protein
Components
  • ORF
  • Protein zyg-11 homolog B
KeywordsVIRAL PROTEIN / auxiliary protein
Function / homology
Function and homology information


Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
: / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Protein zyg-11 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGao, X. / Cui, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharm Sin B / Year: 2024
Title: SARS-CoV-2 ORF10 hijacking ubiquitination machinery reveals potential unique drug targeting sites
Authors: Zhu, K. / Song, L. / Wang, L. / Hua, L. / Luo, Z. / Wang, T. / Qin, B. / Yuan, S. / Gao, X. / Mi, W. / Cui, S.
History
DepositionJun 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: 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.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein zyg-11 homolog B
B: Protein zyg-11 homolog B
C: Protein zyg-11 homolog B
D: Protein zyg-11 homolog B
E: ORF
F: ORF
G: ORF
H: ORF


Theoretical massNumber of molelcules
Total (without water)113,3498
Polymers113,3498
Non-polymers00
Water00
1
A: Protein zyg-11 homolog B
F: ORF


Theoretical massNumber of molelcules
Total (without water)28,3372
Polymers28,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-4 kcal/mol
Surface area10840 Å2
MethodPISA
2
B: Protein zyg-11 homolog B
G: ORF


Theoretical massNumber of molelcules
Total (without water)28,3372
Polymers28,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-4 kcal/mol
Surface area10720 Å2
MethodPISA
3
C: Protein zyg-11 homolog B
E: ORF


Theoretical massNumber of molelcules
Total (without water)28,3372
Polymers28,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-3 kcal/mol
Surface area11110 Å2
MethodPISA
4
D: Protein zyg-11 homolog B
H: ORF


Theoretical massNumber of molelcules
Total (without water)28,3372
Polymers28,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.300, 72.800, 127.500
Angle α, β, γ (deg.)90.000, 113.400, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Protein zyg-11 homolog B


Mass: 27554.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZYG11B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C0D3
#2: Protein/peptide
ORF


Mass: 782.884 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.89→39.65 Å / Num. obs: 19906 / % possible obs: 98.4 % / Redundancy: 3.36 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 4.13
Reflection shellResolution: 2.89→3.07 Å / Num. unique obs: 6197 / CC1/2: 0.12 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EP0

7ep0


Resolution: 2.9→17.05 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 981 4.94 %
Rwork0.2498 18888 -
obs0.2504 19869 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.62 Å2 / Biso mean: 68.3244 Å2 / Biso min: 38.53 Å2
Refinement stepCycle: final / Resolution: 2.9→17.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 0 0 0 7885
Num. residues----979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.050.3881590.36522637279699
3.05-3.240.3151020.338127172819100
3.24-3.490.29861520.299126882840100
3.49-3.840.29051650.266526732838100
3.84-4.380.23421570.231826482805100
4.38-5.490.23771120.229927642876100
5.49-17.050.22681340.20752761289599

+
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