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- EMDB-49950: SARS-CoV M protein dimer in complex with FAb B -

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Basic information

Entry
Database: EMDB / ID: EMD-49950
TitleSARS-CoV M protein dimer in complex with FAb B
Map data
Sample
  • Complex: SARS-CoV M protein dimer in complex with FAb B
    • Protein or peptide: Membrane protein
    • Protein or peptide: FAb B light chain
    • Protein or peptide: FAb B heavy chain
KeywordsM protein / SARS-CoV-2 / inhibitor bound complex / viral protein / MEMBRANE PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / host cell Golgi membrane / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / structural constituent of virion / viral envelope / virion membrane ...Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / host cell Golgi membrane / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / structural constituent of virion / viral envelope / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsMann MK / Abeywickrema P
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201700018C United States
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into MERS and SARS coronavirus membrane proteins.
Authors: Mandeep Kaur Mann / Yanting Yin / Simone Marsili / Jiexiong Xie / Jordi Doijen / Robyn Miller / Madison Piassek / Nick van den Broeck / Christopher Kinyanjui Kariuki / Heidi L M de Gruyter / ...Authors: Mandeep Kaur Mann / Yanting Yin / Simone Marsili / Jiexiong Xie / Jordi Doijen / Robyn Miller / Madison Piassek / Nick van den Broeck / Christopher Kinyanjui Kariuki / Heidi L M de Gruyter / Anouk A Leijs / Eric J Snijder / Martijn J van Hemert / Ken Keustermans / Michiel Van Gool / Xiaodi Yu / Marnix van Loock / Anil Koul / Sujata Sharma / Ellen Van Damme / Pravien Abeywickrema /
Abstract: The membrane (M) protein of coronaviruses is essential for maintaining structural integrity during membrane virion budding and viral pathogenesis. Given its high conservation in lineages within the ...The membrane (M) protein of coronaviruses is essential for maintaining structural integrity during membrane virion budding and viral pathogenesis. Given its high conservation in lineages within the betacoronavirus genus, such as sarbecoviruses, the M protein presents as an attractive therapeutic target; however, developing broad-spectrum antivirals targeting coronaviruses such as MERS-CoV is challenging due to lower sequence conservation and limited structural information available beyond that of the SARS-CoV-2 M protein. In this study, we report 3-3.2 Å resolution structures of MERS-CoV M protein, engineered with a SARS-CoV-2-like antibody interface, representing the first human merbecovirus M protein structure, and SARS-CoV M protein structures, with and without a previously identified SARS-CoV-2 M protein inhibitor, JNJ-9676. We highlight the structural differences between the MERS-CoV, SARS-CoV and SARS-CoV-2 M proteins, and present insights into the conservation of the JNJ-9676 binding pocket as well as key differences that could be targeted to accelerate the design of specific MERS-CoV and broad-spectrum antivirals targeting coronavirus M proteins.
History
DepositionMar 31, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49950.png

Downloads & links

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Map

FileDownload / File: emd_49950.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 288 pix.
= 262.08 Å		0.91 Å/pix.
x 288 pix.
= 262.08 Å		0.91 Å/pix.
x 288 pix.
= 262.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.156
Minimum - Maximum-1.4915814 - 1.8217287
Average (Standard dev.)-0.00018896892 (±0.03395156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 262.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49950_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49950_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV M protein dimer in complex with FAb B

EntireName: SARS-CoV M protein dimer in complex with FAb B
Components
  • Complex: SARS-CoV M protein dimer in complex with FAb B
    • Protein or peptide: Membrane protein
    • Protein or peptide: FAb B light chain
    • Protein or peptide: FAb B heavy chain

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Supramolecule #1: SARS-CoV M protein dimer in complex with FAb B

SupramoleculeName: SARS-CoV M protein dimer in complex with FAb B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 29.889562 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MADNGTITVE ELKQLLEQWN LVIGFLFLAW IMLLQFAYSN RNRFLYIIKL VFLWLLWPVT LACFVLAAVY RINWVTGGIA IAMACIVGL MWLSYFVASF RLFARTRSMW SFNPETNILL NVPLRGTIVT RPLMESELVI GAVIIRGHLR MAGHSLGRCD I KDLPKEIT ...String:
MADNGTITVE ELKQLLEQWN LVIGFLFLAW IMLLQFAYSN RNRFLYIIKL VFLWLLWPVT LACFVLAAVY RINWVTGGIA IAMACIVGL MWLSYFVASF RLFARTRSMW SFNPETNILL NVPLRGTIVT RPLMESELVI GAVIIRGHLR MAGHSLGRCD I KDLPKEIT VATSRTLSYY KLGASQRVGT DSGFAAYNRY RIGNYKLNTD HAGSNDNIAL LVQSNSLEVL FQGPSRGGSG AA AGSGSGS GSPSRLEEEL RRRLTEGSEP EA

UniProtKB: Membrane protein

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Macromolecule #2: FAb B light chain

MacromoleculeName: FAb B light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.157424 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: ASDIVMTQSP ASLAVSLGQR ATISCKASQS IDYDGDNYMN WYQQKPGQPP KLLIYTTSNL ESGIPARFSG SGSGTDFTLN IHPVEEGDA ATYYCQQNNE DPYTFGGGTK LEIKRADAAP TVSIFPPSSE QLTSGGASVV CFLNNFYPKD INVKWKIDGS E RQNGVLNS ...String:
ASDIVMTQSP ASLAVSLGQR ATISCKASQS IDYDGDNYMN WYQQKPGQPP KLLIYTTSNL ESGIPARFSG SGSGTDFTLN IHPVEEGDA ATYYCQQNNE DPYTFGGGTK LEIKRADAAP TVSIFPPSSE QLTSGGASVV CFLNNFYPKD INVKWKIDGS E RQNGVLNS WTDQDSKDST YSMSSTLTLT KDEYERHNSY TCEATHKTST SPIVKSFNRN EC

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Macromolecule #3: FAb B heavy chain

MacromoleculeName: FAb B heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.211092 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: EVQLQQSGPE LVKPGASMKI SCKTSGYSFT GYTMNWVKQS HGKNLEWIGL INPYNGDTSY NQKFKGKATL TVDKSSSTAY MELLSLTSE DSAVYYCEVI NTYWGQGTLV TVSAAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL S SGVHTFPA ...String:
EVQLQQSGPE LVKPGASMKI SCKTSGYSFT GYTMNWVKQS HGKNLEWIGL INPYNGDTSY NQKFKGKATL TVDKSSSTAY MELLSLTSE DSAVYYCEVI NTYWGQGTLV TVSAAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL S SGVHTFPA VLQSDLYTLS SSVTVPSSTW PSETVTCNVA HPASSTKVDK KIVPRDCGSG SHHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vgs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1210771
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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