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- PDB-6w37: STRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 6w37
TitleSTRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
ComponentsORF7a protein
KeywordsVIRAL PROTEIN / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / SARS-CoV-2 modulates autophagy / host cell Golgi membrane / Virion Assembly and Release / suppression by virus of host tetherin activity / 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 ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / SARS-CoV-2 modulates autophagy / host cell Golgi membrane / Virion Assembly and Release / suppression by virus of host tetherin activity / 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 / SARS coronavirus X4 / 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. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsNelson, C.A. / Minasov, G. / Shuvalova, L. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To be published
Title: STRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
Authors: Nelson, C.A. / Minasov, G. / Shuvalova, L. / Fremont, D.H.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2May 20, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.3Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.4Jan 12, 2022Group: Database references / Structure summary / Category: database_2 / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords
Revision 1.5Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF7a protein


Theoretical massNumber of molelcules
Total (without water)7,5391
Polymers7,5391
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.393, 57.393, 55.918
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein ORF7a protein / SARS-Cov-2 Accessory protein 7a / Protein U122 / Protein X4 / ORF7a / Accessory protein 7a / Protein 7a


Mass: 7539.497 Da / Num. of mol.: 1 / Fragment: H-2Kb residues 1-277
Source method: isolated from a genetically manipulated source
Details: refolded
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: 7a / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P0DTC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.53 Å3/Da / Density % sol: 65.12 % / Description: Long thin needles.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 20% PEG 4000, 0.2 M CaCl2, 0.1M Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.48
ReflectionResolution: 2.9→37.15 Å / Num. obs: 2553 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.083 / Rrim(I) all: 0.263 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.0810.71.04242573990.6150.3351.0962.6100
8.7-37.147.30.0888461160.9920.0340.09519.998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.49 Å37.15 Å
Translation4.49 Å37.15 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XAK

1xak


Resolution: 2.9→37.15 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.268 262 10.31 %
Rwork0.2359 --
obs0.2551 2541 99.92 %
Displacement parametersBiso mean: 37.64 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 0 3 525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013537
X-RAY DIFFRACTIONf_angle_d0.4127728
X-RAY DIFFRACTIONf_chiral_restr0.039277
X-RAY DIFFRACTIONf_plane_restr0.001895
X-RAY DIFFRACTIONf_dihedral_angle_d7.6375191
LS refinement shellResolution: 2.9→37.15 Å /
Num. reflection% reflection
Rwork2541 -
obs-99.92 %

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