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- PDB-7jtl: Structure of SARS-CoV-2 ORF8 accessory protein -

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Basic information

Entry
Database: PDB / ID: 7jtl
TitleStructure of SARS-CoV-2 ORF8 accessory protein
ComponentsORF8 protein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / SARS2 / Covid-19 / coronavirus / accessory protein / host-factor restriction / RNA virus / immune evasion / MHC-I / open reading frame 8
Function / homology
Function and homology information


Translation of Accessory Proteins / positive regulation of immunoglobulin mediated immune response / Interleukin-17 signaling / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / negative regulation of interferon-beta production / cytokine activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lysosome / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses ...Translation of Accessory Proteins / positive regulation of immunoglobulin mediated immune response / Interleukin-17 signaling / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / negative regulation of interferon-beta production / cytokine activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lysosome / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding
Similarity search - Function
SARS-like ORF8 accessory protein, Ig-like domain / SARS ORF8 accessory protein immunoglobulin (Ig)-like domain profile. / Non-structural protein ORF8, betacoronavirus / ORF8, SARS-CoV-2 / Betacoronavirus NS8 protein
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsFlower, T.G. / Buffalo, C.Z. / Hooy, R.M. / Allaire, M. / Ren, X. / Hurley, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI112442 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 GM125209 United States
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein.
Authors: Flower, T.G. / Buffalo, C.Z. / Hooy, R.M. / Allaire, M. / Ren, X. / Hurley, J.H.
#1: Journal: Biorxiv / Year: 2020
Title: Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion.
Authors: Flower, T.G. / Buffalo, C.Z. / Hooy, R.M. / Allaire, M. / Ren, X. / Hurley, J.H.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity_name_com ...citation / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Feb 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / citation / citation_author / entity / entity_name_com / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_asym / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_name_com.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Model completeness / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF8 protein
B: ORF8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4713
Polymers24,4482
Non-polymers231
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-16 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.258, 44.258, 264.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain "A" and (resid 18 through 63 or (resid 64...
21(chain "B" and ((resid 18 through 19 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLUAA18 - 641 - 47
12SERILEAA69 - 12150 - 102
21GLNGLUBB18 - 641 - 47
22SERILEBB69 - 12149 - 101

NCS oper: (Code: givenMatrix: (-0.999049108241, 0.030578559849, 0.0310778216764), (-0.0184046261016, -0.941970692597, 0.335190220659), (0.0395240314321, 0.334299515353, 0.941637767389)Vector: 75. ...NCS oper: (Code: given
Matrix: (-0.999049108241, 0.030578559849, 0.0310778216764), (-0.0184046261016, -0.941970692597, 0.335190220659), (0.0395240314321, 0.334299515353, 0.941637767389)
Vector: 75.7226022731, 32.3032306474, -7.30090826968)

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Components

#1: Protein ORF8 protein / ORF8 / Non-structural protein 8 / ns8


Mass: 12223.868 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium dihydrogen phosphate pH 6.5, 12 % (w/v) PEG8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.000001 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000001 Å / Relative weight: 1
ReflectionResolution: 2.04→43.65 Å / Num. obs: 17510 / % possible obs: 95.06 % / Redundancy: 10 % / Biso Wilson estimate: 36.25 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1009 / Rpim(I) all: 0.03226 / Rrim(I) all: 0.1061 / Net I/σ(I): 14.92
Reflection shellResolution: 2.04→2.11 Å / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1593 / CC1/2: 0.39 / Rpim(I) all: 0.555 / Rrim(I) all: 1.694

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.04→43.65 Å / SU ML: 0.2592 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.0001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 1700 10 %
Rwork0.2174 15305 -
obs0.2214 17005 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.47 Å2
Refinement stepCycle: LAST / Resolution: 2.04→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 1 202 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771666
X-RAY DIFFRACTIONf_angle_d0.99092272
X-RAY DIFFRACTIONf_chiral_restr0.0613254
X-RAY DIFFRACTIONf_plane_restr0.007290
X-RAY DIFFRACTIONf_dihedral_angle_d15.1136596
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.47328329025 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.3851180.35991041X-RAY DIFFRACTION79.17
2.1-2.170.34451220.3141100X-RAY DIFFRACTION86.12
2.17-2.250.35311310.30911173X-RAY DIFFRACTION88.95
2.25-2.340.31241360.26621199X-RAY DIFFRACTION91.75
2.34-2.440.32871360.26541243X-RAY DIFFRACTION96.23
2.44-2.570.29991420.26081284X-RAY DIFFRACTION98.01
2.57-2.730.30791480.2511322X-RAY DIFFRACTION99.26
2.73-2.940.30161490.2221337X-RAY DIFFRACTION99.87
2.94-3.240.2121450.21651329X-RAY DIFFRACTION99.93
3.24-3.710.24151540.20231377X-RAY DIFFRACTION100
3.71-4.670.22421530.16211380X-RAY DIFFRACTION100
4.67-43.650.22741660.20961520X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.901640301079-0.3240620178590.7770290462470.550297168245-0.2548083559390.830067999353-0.1723266071090.1935210040120.3931152646240.2825076946010.111659325518-0.151371903135-0.0399292468792-0.183302812714-0.001286882622680.217252432229-0.0175317558673-0.0003789759719880.4822557732570.02675894495380.34467652927950.506586434638.7413898998111.882078392
20.8272086818650.510464922872-0.7892960673910.527050299864-0.3599944008270.811968806507-0.173666715429-0.426798060487-0.4456469773080.0449397165512-0.0542151023022-0.0594929498040.0452852467527-0.111127720912-0.002743832133680.2969127948990.01211545600750.009477112370610.3878548787480.07991827741410.44943461752349.082167878324.3404076581116.881100926
31.426941468231.93864848960.3181829962974.47373838371-0.3762186875320.4313391391580.171551007444-0.37862741180.4136601676540.45942763431-0.5035276714680.6830852589960.03997887556490.454832980708-0.1023397795710.410988768913-0.0197404127980.06891749457650.5709746639330.001784847394960.19738710627851.098593438516.275876224102.004017712
41.10174565390.32690850461-0.3679490928391.800410729610.634035915581.1901549975-0.06910496171490.1497371834250.01744245157950.0504904217133-0.0809490102035-0.09925417341320.101905570720.0763570200729-0.0002861747864220.26138158315-0.007220703395030.005729063919770.395023414170.01923282937540.28674673772149.965550726428.2630136034115.426644307
53.02015054481-2.32746335929-1.07603070763.09229959579-1.067865788063.103688669430.02167285643110.003248781514-0.06746999722910.298461730196-0.0186154026277-0.473241503994-0.09582023765370.06355876595690.0001235758611960.217545842351-0.0185924145870.01792898774560.4343474843050.02249844184860.43219340147830.803530972533.1376995565113.494282135
61.12972148194-1.02173651233-0.1595575486120.9338131334130.3138166425291.21178336173-0.1627847076320.05521182933960.3800891352840.2762133786250.07904042845270.0140458540566-0.259620304393-0.08538125960280.0008640981122850.327837353130.0912890186085-0.1025456294450.3599215419660.01615757624610.3545139103931.515563174347.5337683082112.452207946
70.154906041480.0787860756164-0.2195092479910.181152521075-0.147305960040.3000680578520.3842078443940.6979640895720.5444679680870.249614882575-0.5895733722270.216472871624-0.117963124188-0.314575128567-0.0003183393037970.4783704642410.0643932104334-0.08951516607010.5203058782450.03518562914690.72098814099126.181860452850.1437015197100.341704756
80.8112126915480.7495955442070.3734100599770.6878236636730.2465286769560.714826562139-0.3727081243330.297094337825-0.1121340454230.009159776201160.2500725853890.03919572405670.0833615650568-0.151490777492-0.0004087714248450.286249907605-0.002202246617590.02749217175090.4550754179190.04905592502610.36924125016426.689079104137.7975947378106.615500335
92.347007172520.4001771255230.2002312123240.5476336253710.8311867877031.21617931894-0.342308146587-0.07995532208750.09699396639320.1924246422060.0945907774707-0.0839178931675-0.253288378059-0.133742615925-0.1906130389380.3426466666310.0700868801707-0.1461012228010.29015540757-0.003710710973650.28203099466433.20284671946.7679740066116.535441401
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 32 )AA18 - 321 - 15
22chain 'A' and (resid 33 through 64 )AA33 - 6416 - 47
33chain 'A' and (resid 67 through 76 )AA67 - 7648 - 57
44chain 'A' and (resid 77 through 121 )AA77 - 12158 - 102
55chain 'B' and (resid 18 through 32 )BB18 - 321 - 15
66chain 'B' and (resid 33 through 64 )BB33 - 6416 - 47
77chain 'B' and (resid 65 through 77 )BB65 - 7748 - 57
88chain 'B' and (resid 78 through 95 )BB78 - 9558 - 75
99chain 'B' and (resid 96 through 121 )BB96 - 12176 - 101

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