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- EMDB-49949: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49949
TitleSARS-CoV M protein dimer in complex with JNJ-9676 and FAb B
Map data
Sample
  • Complex: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B
    • Protein or peptide: Membrane protein
    • Protein or peptide: FAb B light chain
    • Protein or peptide: FAb B heavy chain
  • Ligand: (6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-methyl-4-oxo-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-3-carboxamide
  • Ligand: water
KeywordsM protein / SARS-CoV-2 / inhibitor bound complex / viral protein / MEMBRANE PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Biological speciesHomo sapiens (human) / SARS-CoV-2 pseudovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsMann MK / Abeywickrema P
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201700018C United States
CitationJournal: To Be Published
Title: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B
Authors: Mann MK / Abeywickrema P
History
DepositionMar 31, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49949.png

Downloads & links

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Map

FileDownload / File: emd_49949.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-1.5042765 - 1.9561884
Average (Standard dev.)-0.00020667355 (±0.03925609)
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_49949_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_49949_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 JNJ-9676 and FAb B

EntireName: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B
Components
  • Complex: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B
    • Protein or peptide: Membrane protein
    • Protein or peptide: FAb B light chain
    • Protein or peptide: FAb B heavy chain
  • Ligand: (6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-methyl-4-oxo-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-3-carboxamide
  • Ligand: water

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Supramolecule #1: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B

SupramoleculeName: SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: SARS-CoV-2 pseudovirus
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

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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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Macromolecule #4: (6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-...

MacromoleculeName: (6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-methyl-4-oxo-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-3-carboxamide
type: ligand / ID: 4 / Number of copies: 2 / Formula: A1AE8
Molecular weightTheoretical: 497.495 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

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

8w2e

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryos / Number images used: 674469
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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