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- PDB-7ci3: The crystal structure of the SARS-CoV-2 ORF7a ectodomain -

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Basic information

Entry
Database: PDB / ID: 7ci3
TitleThe crystal structure of the SARS-CoV-2 ORF7a ectodomain
ComponentsOrf7a protein
KeywordsVIRAL PROTEIN / Ig-like fold / type-I transmembrane protein / ER membrane / accessory protein
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / SARS-CoV-2 modulates autophagy / virion component => GO:0044423 / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / Virion Assembly and Release / suppression by virus of host tetherin activity / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / SARS-CoV-2 modulates autophagy / virion component => GO:0044423 / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / Virion Assembly and Release / suppression by virus of host tetherin activity / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane
Similarity search - Function
Structural accessory protein ORF7a, SARS-CoV-2-like / Structural accessory protein ORF7a, SARS-CoV-like / ORF7a superfamily, coronavirus / Structural accessory protein ORF7a, SARS-CoV-like, X4e domain / Betacoronavirus NS7A protein / X4e domain profile.
Similarity search - Domain/homology
Accessory protein 7a / ORF7a protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, Z. / Zhou, Z. / Chen, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770801 China
CitationJournal: Iscience / Year: 2021
Title: Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14 + monocytes.
Authors: Zhou, Z. / Huang, C. / Zhou, Z. / Huang, Z. / Su, L. / Kang, S. / Chen, X. / Chen, Q. / He, S. / Rong, X. / Xiao, F. / Chen, J. / Chen, S.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orf7a protein


Theoretical massNumber of molelcules
Total (without water)9,5751
Polymers9,5751
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4530 Å2
Unit cell
Length a, b, c (Å)37.545, 37.545, 56.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Orf7a protein / Nonstructural protein NS7a


Mass: 9574.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: ORF7a, NS7a, orf7a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6C0X2S1, UniProt: P0DTC7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Sodium acetate pH 5.0, 10% PEG 3000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 4481 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.053 / Rrim(I) all: 0.116 / Χ2: 0.938 / Net I/σ(I): 4.7 / Num. measured all: 20004
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.80.6292250.6960.3950.7490.74296.2
2.24-2.282.90.5782050.1040.3930.7040.70899
2.28-2.323.20.4172530.8560.2630.4950.508100
2.32-2.373.40.4432010.8170.2770.5250.44199.5
2.37-2.423.60.52250.8320.2960.5830.47999.6
2.42-2.483.90.5342350.7460.3090.6190.449100
2.48-2.544.20.5522210.8230.3070.6330.477100
2.54-2.614.80.5072150.8980.2560.5680.473100
2.61-2.6950.4762340.8590.2350.5320.599100
2.69-2.775.10.3552150.9130.1750.3960.51100
2.77-2.875.20.3012230.9680.1460.3350.533100
2.87-2.995.10.2082160.9740.1020.2320.584100
2.99-3.124.80.1612470.9760.0820.1810.586100
3.12-3.294.70.1221980.9850.0630.1380.705100
3.29-3.495.30.1032390.990.0490.1140.847100
3.49-3.765.20.0832340.9940.040.0920.943100
3.76-4.145.20.0782060.9930.0380.0860.989100
4.14-4.744.80.062400.9970.0310.0671.061100
4.74-5.975.10.0512150.9990.0250.0570.877100
5.97-504.90.12340.8680.0520.1145.13100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XAK

1xak


Resolution: 2.2→28.14 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 445 9.98 %
Rwork0.2295 4015 -
obs0.2326 4460 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.63 Å2 / Biso mean: 49.4772 Å2 / Biso min: 19.46 Å2
Refinement stepCycle: final / Resolution: 2.2→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms542 0 0 8 550
Biso mean---50.22 -
Num. residues----69
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.520.34091520.28651324147699
2.52-3.170.36041460.300213481494100
3.18-28.140.21341470.195613431490100

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