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- PDB-6vsj: Cryo-electron microscopy structure of mouse coronavirus spike pro... -

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Basic information

Entry
Database: PDB / ID: 6vsj
TitleCryo-electron microscopy structure of mouse coronavirus spike protein complexed with its murine receptor
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 1
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / MHV spike / CEACAM1a / Complex / Glycoprotein
Function / homology
Function and homology information


positive regulation of activation-induced cell death of T cells / CD4-positive, alpha-beta T cell activation / Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / Post-translational modification: synthesis of GPI-anchored proteins / regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / granulocyte colony-stimulating factor signaling pathway ...positive regulation of activation-induced cell death of T cells / CD4-positive, alpha-beta T cell activation / Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / Post-translational modification: synthesis of GPI-anchored proteins / regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / 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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin catabolic process / Cell surface interactions at the vascular wall / common myeloid progenitor cell proliferation / negative regulation of interleukin-1 production / Toll-like receptor binding / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / Peyer's patch development / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of platelet aggregation / bile acid transmembrane transporter activity / cell-cell junction organization / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / negative regulation of vascular permeability / virion binding / negative regulation of bone resorption / wound healing, spreading of cells / negative regulation of cytokine production / ciliary membrane / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / microvillus membrane / bile acid and bile salt transport / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of osteoclast differentiation / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / positive regulation of T cell proliferation / transport vesicle / negative regulation of T cell proliferation / Neutrophil degranulation / protein tyrosine kinase binding / basal plasma membrane / negative regulation of protein kinase activity / adherens junction / positive regulation of JNK cascade / regulation of cell growth / cellular response to insulin stimulus / cell junction / cell-cell junction / virus receptor activity / host cell Golgi apparatus / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / calmodulin binding / protein dimerization activity / apical plasma membrane / endocytosis involved in viral entry into host cell / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / cell surface / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Immunoglobulin domain / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Immunoglobulin domain / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Spike glycoprotein / Cell adhesion molecule CEACAM1 / CEA cell adhesion molecule 1
Similarity search - Component
Biological speciesMurine coronavirus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsShang, J. / Wan, Y.S. / Liu, C. / Yount, B. / Gully, K. / Yang, Y. / Auerbach, A. / Peng, G.Q. / Baric, R. / Li, F.
Funding support United States, 1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Spike glycoprotein
D: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Spike glycoprotein
E: Carcinoembryonic antigen-related cell adhesion molecule 1
C: Spike glycoprotein
F: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,04718
Polymers494,3926
Non-polymers2,65412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area42480 Å2
ΔGint-113 kcal/mol
Surface area152450 Å2

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 141118.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine coronavirus (strain A59) / Strain: A59 / Gene: S, 3 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P11224
#2: Protein Carcinoembryonic antigen-related cell adhesion molecule 1 / Biliary glycoprotein 1 / BGP-1 / Biliary glycoprotein D / MHVR1 / Murine hepatitis virus receptor / MHV-R


Mass: 23678.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ceacam1, Bgp, Bgp1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P31809, UniProt: Q3LFS9*PLUS
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1MHV Spike and CEACAM1a ComplexCOMPLEX#1-#20MULTIPLE SOURCES
2Spike glycoproteinCOMPLEX#11RECOMBINANT
3Carcinoembryonic antigen-related cell adhesion molecule 1COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Murine coronavirus (strain A59)11142A59
22Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Baculovirus expression vector pFastBac1-HM274590
22Baculovirus expression vector pFastBac1-HM274590
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
120 mMTris-HCl1
2200 mMNaCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 77 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82923 / Symmetry type: POINT

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