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- PDB-7yc2: Crystal structure of auxiliary protein in complex with human protein -

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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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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

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