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- EMDB-21377: Cryo-electron microscopy structure of mouse coronavirus spike pro... -

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Entry
Database: EMDB / ID: EMD-21377
TitleCryo-electron microscopy structure of mouse coronavirus spike protein complexed with its murine receptor
Map dataCryoEM density map of MHV spike ectodomain complex with its receptor CEACAM1a
Sample
  • Complex: MHV Spike and CEACAM1a Complex
    • Complex: Spike glycoprotein
      • Protein or peptide: Spike glycoprotein
    • Complex: Carcinoembryonic antigen-related cell adhesion molecule 1
      • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / positive regulation of homophilic cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis ...Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / positive regulation of homophilic cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / regulation of blood vessel remodeling / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / insulin catabolic process / Cell surface interactions at the vascular wall / common myeloid progenitor cell proliferation / Toll-like receptor binding / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of vasculogenesis / bile acid transmembrane transporter activity / regulation of immune system process / negative regulation of platelet aggregation / cell-cell junction organization / negative regulation of vascular permeability / negative regulation of bone resorption / wound healing, spreading of cells / bile acid and bile salt transport / ciliary membrane / negative regulation of cytokine production / microvillus membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of T cell receptor signaling pathway / blood vessel development / negative regulation of osteoclast differentiation / lateral plasma membrane / negative regulation of T cell proliferation / transport vesicle / Neutrophil degranulation / protein tyrosine kinase binding / regulation of ERK1 and ERK2 cascade / basal plasma membrane / regulation of cell growth / adherens junction / negative regulation of protein kinase activity / endocytosis involved in viral entry into host cell / cellular response to insulin stimulus / cell-cell junction / cell junction / virus receptor activity / host cell Golgi apparatus / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / protein dimerization activity / calmodulin binding / cell adhesion / apical plasma membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein kinase binding / host cell plasma membrane / virion membrane / cell surface / signal transduction / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...: / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Carcinoembryonic antigen-related cell adhesion molecule 1 / CEA cell adhesion molecule 1
Similarity search - Component
Biological speciesMurine coronavirus (strain A59) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsShang J / Wan YS / Liu C / Yount B / Gully K / Yang Y / Auerbach A / Peng GQ / Baric R / Li F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI089728 United States
CitationJournal: PLoS Pathog / Year: 2020
Title: Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry.
Authors: Jian Shang / Yushun Wan / Chang Liu / Boyd Yount / Kendra Gully / Yang Yang / Ashley Auerbach / Guiqing Peng / Ralph Baric / Fang Li /
Abstract: Coronaviruses recognize a variety of receptors using different domains of their envelope-anchored spike protein. How these diverse receptor recognition patterns affect viral entry is unknown. Mouse ...Coronaviruses recognize a variety of receptors using different domains of their envelope-anchored spike protein. How these diverse receptor recognition patterns affect viral entry is unknown. Mouse hepatitis coronavirus (MHV) is the only known coronavirus that uses the N-terminal domain (NTD) of its spike to recognize a protein receptor, CEACAM1a. Here we determined the cryo-EM structure of MHV spike complexed with mouse CEACAM1a. The trimeric spike contains three receptor-binding S1 heads sitting on top of a trimeric membrane-fusion S2 stalk. Three receptor molecules bind to the sides of the spike trimer, where three NTDs are located. Receptor binding induces structural changes in the spike, weakening the interactions between S1 and S2. Using protease sensitivity and negative-stain EM analyses, we further showed that after protease treatment of the spike, receptor binding facilitated the dissociation of S1 from S2, allowing S2 to transition from pre-fusion to post-fusion conformation. Together these results reveal a new role of receptor binding in MHV entry: in addition to its well-characterized role in viral attachment to host cells, receptor binding also induces the conformational change of the spike and hence the fusion of viral and host membranes. Our study provides new mechanistic insight into coronavirus entry and highlights the diverse entry mechanisms used by different viruses.
History
DepositionFeb 11, 2020-
Header (metadata) releaseMar 4, 2020-
Map releaseMar 4, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00869
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00869
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vsj
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21377.png

Downloads & links

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Map

FileDownload / File: emd_21377.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density map of MHV spike ectodomain complex with its receptor CEACAM1a
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00869 / Movie #1: 0.00869
Minimum - Maximum-0.042848907 - 0.08298864
Average (Standard dev.)-0.00014359807 (±0.0025173603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0430.083-0.000

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Supplemental data

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Mask #1

Fileemd_21377_msk_1.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 : MHV Spike and CEACAM1a Complex

EntireName: MHV Spike and CEACAM1a Complex
Components
  • Complex: MHV Spike and CEACAM1a Complex
    • Complex: Spike glycoprotein
      • Protein or peptide: Spike glycoprotein
    • Complex: Carcinoembryonic antigen-related cell adhesion molecule 1
      • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: MHV Spike and CEACAM1a Complex

SupramoleculeName: MHV Spike and CEACAM1a Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Murine coronavirus (strain A59) / Strain: A59

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Supramolecule #2: Spike glycoprotein

SupramoleculeName: Spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM

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Supramolecule #3: Carcinoembryonic antigen-related cell adhesion molecule 1

SupramoleculeName: Carcinoembryonic antigen-related cell adhesion molecule 1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine coronavirus (strain A59) / Strain: A59
Molecular weightTheoretical: 141.118797 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MKFLVNVALV FMVVYISYIY AYIGDFRCIQ LVNSNGANVS APSISTETVE VSQGLGTYYV LDRVYLNATL LLTGYYPVDG SKFRNLALR GTNSVSLSWF QPPYLNQFND GIFAKVQNLK TSTPSGATAY FPTIVIGSLF GYTSYTVVIE PYNGVIMASV C QYTICQLP ...String:
MKFLVNVALV FMVVYISYIY AYIGDFRCIQ LVNSNGANVS APSISTETVE VSQGLGTYYV LDRVYLNATL LLTGYYPVDG SKFRNLALR GTNSVSLSWF QPPYLNQFND GIFAKVQNLK TSTPSGATAY FPTIVIGSLF GYTSYTVVIE PYNGVIMASV C QYTICQLP YTDCKPNTNG NKLIGFWHTD VKPPICVLKR NFTLNVNADA FYFHFYQHGG TFYAYYADKP SATTFLFSVY IG DILTQYY VLPFICNPTA GSTFAPRYWV TPLVKRQYLF NFNQKGVITS AVDCASSYTS EIKCKTQSML PSTGVYELSG YTV QPVGVV YRRVANLPAC NIEEWLTARS VPSPLNWERK TFQNCNFNLS SLLRYVQAES LFCNNIDASK VYGRCFGSIS VDKF AVPRS RQVDLQLGNS GFLQTANYKI DTAATSCQLH YTLPKNNVTI NNHNPSSWNR RYGFNDAGVF GKNQHDVVYA QQCFT VRSS FCPCAQPDIV SPCTTQTKPK SAFVNVGDHC EGLGVLEDNC GNADPHKGCI CANNSFIGWS HDTCLVNDRC QIFANI LLN GINSGTTCST DLQLPNTEVV TGICVKYDLY GITGQGVFKE VKADYYNSWQ TLLYDVNGNL NGFRDLTTNK TYTIRSC YS GRVSAAFHKD APEPALLYRN INCSYVFSNN ISREENPLNY FDSYLGCVVN ADNRTDEALP NCDLRMGAGL CVDYSKSR R AHRSVSTGYR LTTFEPYTPM LVNDSVQSVD GLYEMQIPTN FTIGHHEEFI QTRSPKVTID CAAFVCGDNT ACRQQLVEY GSFCVNVNAI LNEVNNLLDN MQLQVASALM QGVTISSRLP DGISGPIDDI NFSPLLGCIG STCAEDGNGP SAIRGRSAIE DLLFDKVKL SDVGFVEAYN NCTGGQEVRD LLCVQSFNGI KVLPPVLSES QISGYTTGAT AAAMFPPWSA AAGVPFSLSV Q YRINGLGV TMNVLSENQK MIASAFNNAL GAIQDGFDAT NSALGKIQSV VNANAEALNN LLNQLSNRFG AISASLQEIL TR LEAVEAK AQIDRLINGR LTALNAYISK QLSDSTLIKV SAAQAIEKVN ECVKSQTTRI NFCGNGNHIL SLVQNAPYGL YFI HFSYVP ISFTTANVSP GLCISGDRGL APKAGYFVQD DGEWKFTGSS YYYPEPITDK NSVIMSSCAV NYTKAPEVFL NTSI PNPPD FKEELDKWFK NQTSIAPDLS LDFEKLNVTL IKRMKQIEDK IEEIESKQKK IENEIARIKK IKHHHHHHHH

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Macromolecule #2: Carcinoembryonic antigen-related cell adhesion molecule 1

MacromoleculeName: Carcinoembryonic antigen-related cell adhesion molecule 1
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.678691 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: EVTIEAVPPQ VAEDNNVLLL VHNLPLALGA FAWYKGNTTA IDKEIARFVP NSNMNFTGQA YSGREIIYSN GSLLFQMITM KDMGVYTLD MTDENYRRTQ ATVRFHVHQP VTQPFLQVTN TTVKELDSVT LTCLSNDIGA NIQWLFNSQS LQLTERMTLS Q NNSILRID ...String:
EVTIEAVPPQ VAEDNNVLLL VHNLPLALGA FAWYKGNTTA IDKEIARFVP NSNMNFTGQA YSGREIIYSN GSLLFQMITM KDMGVYTLD MTDENYRRTQ ATVRFHVHQP VTQPFLQVTN TTVKELDSVT LTCLSNDIGA NIQWLFNSQS LQLTERMTLS Q NNSILRID PIKREDAGEY QCEISNPVSV RRSNSIKLDI IFDPHHHHHH

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.3 mg/mL
BufferpH: 7.4 / Component:
ConcentrationName
20.0 mMTris-HCl
200.0 mMNaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 77.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82923
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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