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- PDB-7y9b: Crystal structure of the membrane (M) protein of a SARS-COV-2-rel... -

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Basic information

Entry
Database: PDB / ID: 7y9b
TitleCrystal structure of the membrane (M) protein of a SARS-COV-2-related coronavirus
ComponentsMembrane protein
KeywordsMEMBRANE PROTEIN / M protein / SARS-COV-2 related
Function / homology
Function and homology information


host cell Golgi membrane / structural constituent of virion / membrane => GO:0016020 / virus-mediated perturbation of host defense response / viral envelope / virion membrane
Similarity search - Function
M matrix/glycoprotein, MERS-like-CoV / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile.
Similarity search - Domain/homology
Biological speciesPipistrellus bat coronavirus HKU5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.214 Å
AuthorsWang, X. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: Pnas Nexus / Year: 2023
Title: Crystal structure of the membrane (M) protein from a bat betacoronavirus.
Authors: Wang, X. / Yang, Y. / Sun, Z. / Zhou, X.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 23, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct / struct_asym / struct_ncs_dom / struct_ncs_dom_lim
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 / _citation.title / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _struct.title
Description: Ligand identity
Details: One reviewer pointed out that an ammonium ion placement in the original model was not conclusive, and suggested us to remove the ammonium ion. Therefore, we have removed the ammonium ion and ...Details: One reviewer pointed out that an ammonium ion placement in the original model was not conclusive, and suggested us to remove the ammonium ion. Therefore, we have removed the ammonium ion and have updated the coordinate file accordingly.
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 1, 2023Group: 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 / _citation_author.identifier_ORCID
Revision 2.2Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.3May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.4Nov 29, 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: Membrane protein
B: Membrane protein
C: Membrane protein
D: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3228
Polymers98,9204
Non-polymers1,4024
Water724
1
A: Membrane protein
B: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1614
Polymers49,4602
Non-polymers7012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-65 kcal/mol
Surface area18330 Å2
MethodPISA
2
C: Membrane protein
D: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1614
Polymers49,4602
Non-polymers7012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-69 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.569, 66.571, 112.628
Angle α, β, γ (deg.)90.00, 109.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Membrane protein / / M protein / E1 glycoprotein / Matrix glycoprotein / Membrane glycoprotein


Mass: 24729.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pipistrellus bat coronavirus HKU5 / Gene: M, 5 / Production host: Komagataella pastoris (fungus) / References: UniProt: A3EXD6
#2: Chemical
ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.8
Details: 300 mM ammonium formate, 50 mM Tris-HCl pH 8.8, 35% PEG 500 MME, 7.1 mM pentaethylene glycol monooctyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.194→48.878 Å / Num. obs: 16908 / % possible obs: 94.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 58.69 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.094 / Rrim(I) all: 0.175 / Net I/σ(I): 6.9 / Num. measured all: 56567
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
3.194-3.2523.20.69726928460.7640.4530.8351.691.9
8.904-48.8783.10.03525808440.9980.0250.04319.395.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y96

7y96


Resolution: 3.214→37.09 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2931 766 4.62 %
Rwork0.2709 --
obs0.2719 16586 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.214→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5928 0 96 4 6028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026201
X-RAY DIFFRACTIONf_angle_d0.4128427
X-RAY DIFFRACTIONf_dihedral_angle_d12.4413598
X-RAY DIFFRACTIONf_chiral_restr0.04969
X-RAY DIFFRACTIONf_plane_restr0.003999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.214-3.46180.33481620.32493117X-RAY DIFFRACTION94
3.4618-3.80990.33761630.30063072X-RAY DIFFRACTION93
3.8099-4.36040.30371510.27273050X-RAY DIFFRACTION91
4.3604-5.49080.27381490.25933255X-RAY DIFFRACTION97
5.4908-37.090.23921410.23793326X-RAY DIFFRACTION96

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