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- EMDB-30418: Cryo-EM structure of PCoV_GX spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-30418
TitleCryo-EM structure of PCoV_GX spike glycoprotein
Map data
Sample
  • Complex: PCoV_GX glycoprotein
    • Protein or peptide: Glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesPangolin coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWang X / Yu J / Zhang S / Qiao S / Zeng J / Tian L
CitationJournal: Nat Commun / Year: 2021
Title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution.
Authors: Shuyuan Zhang / Shuyuan Qiao / Jinfang Yu / Jianwei Zeng / Sisi Shan / Long Tian / Jun Lan / Linqi Zhang / Xinquan Wang /
Abstract: In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species ...In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the "down" conformation, indicating they are more prone to adopt the receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. We further identified critical residues in the RBD underlying different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes. These results collectively indicate that tight RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.
History
DepositionJul 30, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 24, 2021-
Current statusMar 24, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cn8
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30418.png

Downloads & links

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Map

FileDownload / File: emd_30418.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.0077 / Movie #1: 0.014
Minimum - Maximum-0.052762438 - 0.11783081
Average (Standard dev.)0.00026490836 (±0.0029988498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 320.41998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.08251.08251.0825
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z320.420320.420320.420
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS296296296
D min/max/mean-0.0530.1180.000

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Supplemental data

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Sample components

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Entire : PCoV_GX glycoprotein

EntireName: PCoV_GX glycoprotein
Components
  • Complex: PCoV_GX glycoprotein
    • Protein or peptide: Glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID

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Supramolecule #1: PCoV_GX glycoprotein

SupramoleculeName: PCoV_GX glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pangolin coronavirus
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pangolin coronavirus
Molecular weightTheoretical: 143.501922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLFVLPL VSSQCVNLTT RTGIPPGYTN SSTRGVYYPD KVFRSSILHL TQDLFLPFFS NVTWFNTINY QGGFKKFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD ARTQSLLIVN NATNVVIKVC EFQFCTDPFL GVYYHNNNKT WVENEFRVYS S ANNCTFEY ...String:
MFVFLFVLPL VSSQCVNLTT RTGIPPGYTN SSTRGVYYPD KVFRSSILHL TQDLFLPFFS NVTWFNTINY QGGFKKFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD ARTQSLLIVN NATNVVIKVC EFQFCTDPFL GVYYHNNNKT WVENEFRVYS S ANNCTFEY ISQPFLMDLE GKQGNFKNLR EFVFKNVDGY FKIYSKHTPI DLVRDLPRGF AALEPLVDLP IGINITRFQT LL ALHRSYL TPGNLESGWT TGAAAYYVGY LQQRTFLLSY NQNGTITDAV DCSLDPLSET KCTLKSLTVE KGIYQTSNFR VQP TISIVR FPNITNLCPF GEVFNASKFA SVYAWNRKRI SNCVADYSVL YNSTSFSTFK CYGVSPTKLN DLCFTNVYAD SFVV KGDEV RQIAPGQTGV IADYNYKLPD DFTGCVIAWN SVKQDALTGG NYGYLYRLFR KSKLKPFERD ISTEIYQAGS TPCNG QVGL NCYYPLERYG FHPTTGVNYQ PFRVVVLSFE LLNGPATVCG PKLSTTLVKD KCVNFNFNGL TGTGVLTTSK KQFLPF QQF GRDISDTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQDV NCTEVPMAIH AEQLTPAWRV YSAGANV FQ TRAGCLVGAE HVNNSYECDI PVGAGICASY HSMSSLRSVN QRSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEI L PVSMTKTSVD CTMYICGDSI ECSNLLLQYG SFCTQLNRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKDF GGFNFSQIL PDPSKPSKRS FIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQ IPFAMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALNTLVKQ L SSNFGAIS SVLNDILSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KG YHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPAICH EGKAHFPREG VFVSNGTHWF ITQRNFYEPQ IITTDNTFVS GSC DVVIGI VNNTVYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESPIDLQE LGKY EQYIK GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE KGSDYKDDDD K

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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: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #4: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 4 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID / Linoleic acid

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263901
FSC plot (resolution estimation)

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