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- PDB-7y96: Crystal structure of the carboxy-terminal domain of a coronavirus... -

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Basic information

Entry
Database: PDB / ID: 7y96
TitleCrystal structure of the carboxy-terminal domain of a coronavirus M protein fused with a split GFP
ComponentsGreen fluorescent protein,Membrane protein
KeywordsMEMBRANE PROTEIN / M protein / Cytosolic domain / SARS-COV-2 related
Function / homology
Function and homology information


host cell Golgi membrane / bioluminescence / generation of precursor metabolites and energy / 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. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Membrane protein / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Pipistrellus bat coronavirus HKU5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.415 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 1.1Mar 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 1.2Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 31, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 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: Green fluorescent protein,Membrane protein
B: Green fluorescent protein,Membrane protein


Theoretical massNumber of molelcules
Total (without water)76,2362
Polymers76,2362
Non-polymers00
Water00
1
A: Green fluorescent protein,Membrane protein

B: Green fluorescent protein,Membrane protein

A: Green fluorescent protein,Membrane protein

B: Green fluorescent protein,Membrane protein


Theoretical massNumber of molelcules
Total (without water)152,4724
Polymers152,4724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation8_455x-y-1,-y,-z1
Unit cell
Length a, b, c (Å)82.020, 82.020, 427.841
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 2 through 232 or resid 242 through 322))

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAchain AAA2 - 3222 - 320
21ARGARG(chain B and (resid 2 through 232 or resid 242 through 322))BB2 - 2322 - 230
22ALAALA(chain B and (resid 2 through 232 or resid 242 through 322))BB242 - 322240 - 320

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Components

#1: Protein Green fluorescent protein,Membrane protein / M protein / E1 glycoprotein / Matrix glycoprotein / Membrane glycoprotein


Mass: 38118.020 Da / Num. of mol.: 2 / Fragment: carboxy-terminal domain / Mutation: R30S,Y39N,M153T,V163A,I171A,A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Pipistrellus bat coronavirus HKU5
Gene: GFP, M, 5 / Production host: Komagataella pastoris (fungus) / References: UniProt: P42212, UniProt: A3EXD6
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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.3, PEG 3350 27%, 0.5% ethyl acetate

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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: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.4→46.33 Å / Num. obs: 11907 / % possible obs: 93.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 70.96 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.077 / Rrim(I) all: 0.169 / Net I/σ(I): 8.9 / Num. measured all: 52103
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
3.4-3.4624.50.56326985960.8210.280.6322.793.9
9.437-46.3340.04123615950.9970.0220.0472380.2

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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: 2B3Q

2b3q


Resolution: 3.415→38.292 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 555 4.72 %
Rwork0.2397 11207 -
obs0.2409 11762 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.48 Å2 / Biso mean: 65.0833 Å2 / Biso min: 38.64 Å2
Refinement stepCycle: final / Resolution: 3.415→38.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 0 0 4890
Num. residues----623
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2764X-RAY DIFFRACTION14.067TORSIONAL
12B2764X-RAY DIFFRACTION14.067TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4151-3.75850.35811330.3035275996
3.7585-4.30170.26191430.2554277096
4.3017-5.41730.2131440.204278594
5.4173-38.2920.26911350.2299289390
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)
12.3029-0.93970.43182.5267-1.0131.61520.2383-0.31640.1664-0.9004-0.56480.3034-0.22460.2684-0.07850.56350.1473-0.1270.96170.0350.8213-43.61822.3214-18.7378
24.3371-1.46661.30081.7533-1.12851.5695-0.3397-0.85170.93420.21770.4444-0.5732-0.10780.5554-0.07420.31850.03060.00970.9383-0.13440.7871-51.539910.4752-17.7306
31.4364-0.60560.84630.2208-0.27710.92020.07860.30930.1850.1229-0.1206-0.1057-0.13280.1695-0.00870.61760.0299-0.10080.53310.00610.5106-79.2723-6.2621-13.8779
41.03680.1899-0.52882.7531-1.01923.0437-0.07080.1391-0.2867-0.6319-0.2358-0.5210.3-0.38560.23330.70850.1065-0.04240.34460.01320.4054-91.0376-11.2941-20.377
51.33330.47750.63161.54121.01230.7210.0258-0.06660.1542-0.1538-0.0989-0.0629-0.33170.1330.03540.48570.09160.00940.7232-0.08990.6301-56.118310.1265-28.6447
61.0992-0.46810.04181.4578-0.21531.3965-0.5013-1.0970.16360.43380.13480.0111-0.335-0.16860.28570.56260.21450.00981.1839-0.01840.7907-57.07223.4384-11.8587
72.29920.01780.76341.73320.2112.90490.11810.10010.29940.0825-0.09860.1976-0.3372-0.23670.00170.35790.14710.06540.27490.01610.3519-15.949622.5121-19.2586
80.3842-0.278-0.37380.10970.2910.35750.046-0.0504-0.0739-0.0560.0551-0.0264-0.07740.2096-0.11950.5470.03110.00340.6170.02110.48955.19150.765-10.4582
92.00430.01710.7261.0659-0.64391.5809-0.3243-0.8920.24280.14330.8416-0.40050.54320.5464-0.1960.57880.11230.06581.08950.08670.5649-9.601119.0998-0.5874
101.12690.2371-0.26512.2344-0.07771.30590.0809-0.02230.01410.0513-0.2036-0.1768-0.24880.03410.0660.3820.09970.01720.46480.11530.3618-10.356818.4343-16.595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )A2 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 147 )A23 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 192 )A148 - 192
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 231 )A193 - 231
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 293 )A232 - 293
6X-RAY DIFFRACTION6chain 'A' and (resid 294 through 322 )A294 - 322
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 138 )B2 - 138
8X-RAY DIFFRACTION8chain 'B' and (resid 139 through 231 )B139 - 231
9X-RAY DIFFRACTION9chain 'B' and (resid 232 through 254 )B232 - 254
10X-RAY DIFFRACTION10chain 'B' and (resid 255 through 322 )B255 - 322

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