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- PDB-9dcj: Pentameric Structure of MERS-CoV Envelope Protein Transmembrane D... -

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Basic information

Entry
Database: PDB / ID: 9dcj
TitlePentameric Structure of MERS-CoV Envelope Protein Transmembrane Domain Determined by Solid-State NMR
ComponentsEnvelope small membrane protein
KeywordsVIRAL PROTEIN / viroporin / MERS-CoV
Function / homology
Function and homology information


disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / host cell Golgi membrane / host cell Golgi apparatus / membrane
Similarity search - Function
Envelope small membrane protein, MERS-CoV-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile.
Similarity search - Domain/homology
Envelope small membrane protein
Similarity search - Component
Biological speciesBetacoronavirus England 1
MethodSOLID-STATE NMR / simulated annealing
AuthorsSucec, I. / Hong, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)6951834 United States
CitationJournal: To Be Published
Title: Structural Insights and Ion Conduction of the MERS-CoV Envelope Protein
Authors: Sucec, I. / Hong, M.
History
DepositionAug 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope small membrane protein
B: Envelope small membrane protein
C: Envelope small membrane protein
D: Envelope small membrane protein
E: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)21,5465
Polymers21,5465
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Envelope small membrane protein / E protein / sM protein


Mass: 4309.228 Da / Num. of mol.: 5 / Mutation: C23S, C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betacoronavirus England 1 / Strain: isolate United Kingdom/H123990006/2012 / Gene: E, sM, 4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K9N5R3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D NCaCx
121isotropic13D NCOCX
131isotropic13D CoNCa
141isotropic12D CC 100 ms
151isotropic33D CCC
1201isotropic33D NCaCx
162isotropic32D CC 300 ms
173isotropic22D NhhC 2 ms
185isotropic12D NhhC 2 ms
1175isotropic12D CC 300 ms
494isotropic21D CODEX
4108isotropic21D CODEX
4116isotropic21D CODEX
1124isotropic22D HF HETCOR
5137isotropic12D DIPSHIFT
1141isotropic12D NCa water-ed
2181isotropic12D CC 24 ms
2151isotropic12D NCa water-ed
3191isotropic12D CC 24 ms
3161isotropic12D NCa water-ed

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
liposome115 % w/w [U-13C; U-15N] MERS ENTM, 23 % w/w POPC, 10 % w/w POPE, 11 % w/w POPS, 4 % w/w cholesterol, 38 % w/w water, 95% H2O/5% D2OP:L=1:25; POPC/POPE/POPS/chol.U-13C, 15N95% H2O/5% D2O
liposome28 % w/w 1,3-glycerol, 2-glycerol 13C MERS ENTM, 21 % w/w POPC, 9 % w/w POPE, 10 % w/w POPS, 4 % w/w cholesterol, 41 % w/w water, 95% H2O/5% D2OP:L=1:18; POPC/POPE/POPS/chol.mixed 1,3-13C : 2-13C, 15N (1:1)95% H2O/5% D2O
liposome38 % w/w [U-13C; U-15N] MERS ENTM, 21 % w/w POPC, 9 % w/w POPE, 10 % w/w POPS, 4 % w/w cholesterol, 41 % w/w water, 95% H2O/5% D2OP:L=1:18; POPC/POPE/POPS/chol.mixed 15N : 13C (1:1)95% H2O/5% D2O
liposome58 % w/w 1,3 glycerol [U-13C; U-15N] MERS ENTM, 21 % w/w POPC, 9 % w/w POPE, 10 % w/w POPS, 4 % w/w cholesterol, 41 % w/w water, 95% H2O/5% D2OP:L=1:18; POPC/POPE/POPS/chol.mixed 1,3-13C : 15N (1:1)95% H2O/5% D2O
liposome417 % w/w 19F MERS ENTM, 21 % w/w POPC, 9 % w/w POPE, 9 % w/w POPS, 3 % w/w cholesterol, 40 % w/w water, 95% H2O/5% D2OP:L=1:15; POPC/POPE/POPS/chol.19F-Phe19 1:1595% H2O/5% D2O
liposome820 % w/w 19F MERS ENTM, 19 % w/w POPC, 8 % w/w POPE, 9 % w/w POPS, 3 % w/w cholesterol, 40 % w/w water, 95% H2O/5% D2OP:L=1:12; POPC/POPE/POPS/chol.19F-Phe19 1:1295% H2O/5% D2O
liposome610 % w/w 19F MERS ENTM, 24 % w/w POPC, 10 % w/w POPE, 11 % w/w POPS, 4 % w/w cholesterol, 40 % w/w water, 95% H2O/5% D2OP:L=1:30; POPC/POPE/POPS/chol.19F-Phe19 1:3095% H2O/5% D2O
liposome715 % w/w [U-13C; U-15N] MERS ENTM, 38 % w/w POPC, 10 % w/w POPG, 38 % w/w water, 95% H2O/5% D2OP:L=1:18; POPC/POPGU-13C, 15N; POPC/POPG95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 % w/wMERS ENTM[U-13C; U-15N]1
23 % w/wPOPCnatural abundance1
10 % w/wPOPEnatural abundance1
11 % w/wPOPSnatural abundance1
4 % w/wcholesterolnatural abundance1
38 % w/wwaternatural abundance1
8 % w/wMERS ENTM1,3-glycerol, 2-glycerol 13C2
21 % w/wPOPCnatural abundance2
9 % w/wPOPEnatural abundance2
10 % w/wPOPSnatural abundance2
4 % w/wcholesterolnatural abundance2
41 % w/wwaternatural abundance2
8 % w/wMERS ENTM[U-13C; U-15N]3
21 % w/wPOPCnatural abundance3
9 % w/wPOPEnatural abundance3
10 % w/wPOPSnatural abundance3
4 % w/wcholesterolnatural abundance3
41 % w/wwaternatural abundance3
8 % w/wMERS ENTM1,3 glycerol [U-13C; U-15N]5
21 % w/wPOPCnatural abundance5
9 % w/wPOPEnatural abundance5
10 % w/wPOPSnatural abundance5
4 % w/wcholesterolnatural abundance5
41 % w/wwaternatural abundance5
17 % w/wMERS ENTM19F4
21 % w/wPOPCnatural abundance4
9 % w/wPOPEnatural abundance4
9 % w/wPOPSnatural abundance4
3 % w/wcholesterolnatural abundance4
40 % w/wwaternatural abundance4
20 % w/wMERS ENTM19F8
19 % w/wPOPCnatural abundance8
8 % w/wPOPEnatural abundance8
9 % w/wPOPSnatural abundance8
3 % w/wcholesterolnatural abundance8
40 % w/wwaternatural abundance8
10 % w/wMERS ENTM19F6
24 % w/wPOPCnatural abundance6
10 % w/wPOPEnatural abundance6
11 % w/wPOPSnatural abundance6
4 % w/wcholesterolnatural abundance6
40 % w/wwaternatural abundance6
15 % w/wMERS ENTM[U-13C; U-15N]7
38 % w/wPOPCnatural abundance7
10 % w/wPOPGnatural abundance7
38 % w/wwaternatural abundance7
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
10.025 MpH 7.4, 20 mM tris, 20 mM NaCl7.41 atm290 K
20.1 MpH 4.5, 25 mM NaOAc,25 mM NaCl + 25 mM CaCl24.51 atm286 K
30.2 MpH 7.5 20 mM tris + 200 mM KCl7.51 atm288 K
40.025 M-20C7.41 atm253 KpH 7.4, 20 mM tris, 20 mM NaCl
50.025 M30C7.41 atm303 KpH 7.4, 20 mM tris, 20 mM NaCl

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE NEOBrukerAVANCE NEO6003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysisv3CCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospincollection
CcpNmr Analysisv3CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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