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- PDB-9nz5: MERSmut-CoV M protein dimer in complex with FAb B -

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Basic information

Entry
Database: PDB / ID: 9nz5
TitleMERSmut-CoV M protein dimer in complex with FAb B
Components
  • FAb B heavy chain
  • FAb B light chain
  • Membrane protein
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM/INHIBITOR / M protein / SARS-CoV-2 / inhibitor bound complex / viral protein / MEMBRANE PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


host cell Golgi membrane / structural constituent of virion / viral envelope / virion membrane / 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 speciesMiddle East respiratory syndrome-related coronavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMann, M.K. / Abeywickrema, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201700018C United States
CitationJournal: To Be Published
Title: MERSmut-CoV M protein dimer in complex with FAb B
Authors: Mann, M.K. / Abeywickrema, P.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane protein
D: Membrane protein
C: FAb B light chain
B: FAb B heavy chain
E: FAb B light chain
F: FAb B heavy chain


Theoretical massNumber of molelcules
Total (without water)155,8216
Polymers155,8216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 29542.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Gene: M, E, AL079_478421_M
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: R9UNX5
#2: Antibody FAb B light chain


Mass: 24157.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
#3: Antibody FAb B heavy chain


Mass: 24211.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MERSmut-CoV M protein dimer in complex with FAb B / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2300 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 51.96 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 827876 / Symmetry type: POINT
RefinementHighest resolution: 3.15 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049940
ELECTRON MICROSCOPYf_angle_d0.83913565
ELECTRON MICROSCOPYf_dihedral_angle_d4.881356
ELECTRON MICROSCOPYf_chiral_restr0.0511541
ELECTRON MICROSCOPYf_plane_restr0.0081704

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