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- EMDB-32960: MERS-CoV spike complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32960
TitleMERS-CoV spike complex
Map data
Sample
  • Complex: MERS-CoV Spike
    • Protein or peptide: Spike glycoproteinSpike protein
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / 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, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 speciesMiddle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsZeng JW / Zhang SY / Wang XW
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFC0845900 China
CitationJournal: Front Microbiol / Year: 2022
Title: Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein.
Authors: Shuyuan Zhang / Wenxv Jia / Jianwei Zeng / Mingxi Li / Ziyi Wang / Haixia Zhou / Linqi Zhang / Xinquan Wang /
Abstract: Neutralizing monoclonal antibodies (mAbs) against highly pathogenic coronaviruses represent promising candidates for clinical intervention. Here, we isolated a potent neutralizing monoclonal ...Neutralizing monoclonal antibodies (mAbs) against highly pathogenic coronaviruses represent promising candidates for clinical intervention. Here, we isolated a potent neutralizing monoclonal antibody, MERS-S41, from a yeast displayed scFv library using the S protein as a bait. To uncover the neutralization mechanism, we determined structures of MERS-S41 Fab in complex with the trimeric spike glycoprotein by cryoelectron microscopy (cryo-EM). We observed four distinct classes of the complex structure, which showed that the MERS-S41 Fab bound to the "up" receptor binding domain (RBD) with full saturation and also bound to an accessible partially lifted "down" RBD, providing a structural basis for understanding how mAbs bind to trimeric spike glycoproteins. Structure analysis of the epitope and cell surface staining assays demonstrated that virus entry is blocked predominantly by direct competition with the host receptor, dipeptidyl peptidase-4 (DPP4).
History
DepositionFeb 25, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32960.png

Downloads & links

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Map

FileDownload / File: emd_32960.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.034202773 - 0.10493815
Average (Standard dev.)0.00012763712 (±0.0019604017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32960_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32960_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32960_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MERS-CoV Spike

EntireName: MERS-CoV Spike
Components
  • Complex: MERS-CoV Spike
    • Protein or peptide: Spike glycoproteinSpike protein

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Supramolecule #1: MERS-CoV Spike

SupramoleculeName: MERS-CoV Spike / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

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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: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 133.079141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ...String:
TVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ILEPRSGNHC PAGNSYTSFA TYHTPATDCS DGNYNRNASL NSFKEYFNLR NCTFMYTYNI TEDEILEWFG IT QTAQGVH LFSSRYVDLY GGNMFQFATL PVYDTIKYYS IIPHSIRSIQ SDRKAWAAFY VYKLQPLTFL LDFSVDGYIR RAI DCGFND LSQLHCSYES FDVESGVYSV SSFEAKPSGS VVEQAEGVEC DFSPLLSGTP PQVYNFKRLV FTNCNYNLTK LLSL FSVND FTCSQISPAA IASNCYSSLI LDYFSYPLSM KSDLSVSSAG PISQFNYKQS FSNPTCLILA TVPHNLTTIT KPLKY SYIN KCSRFLSDDR TEVPQLVNAN QYSPCVSIVP STVWEDGDYY RKQLSPLEGG GWLVASGSTV AMTEQLQMGF GITVQY GTD TNSVCPKLEF ANDTKIASQL GNCVEYSLYG VSGRGVFQNC TAVGVRQQRF VYDAYQNLVG YYSDDGNYYC LRACVSV PV SVIYDKETKT HATLFGSVAC EHISSTMSQY SRSTRSMLKR RDSTYGPLQT PVGCVLGLVN SSLFVEDCKL PLGQSLCA L PDTPSTLTPR SVRSVPGEMR LASIAFNHPI QVDQLNSSYF KLSIPTNFSF GVTQEYIQTT IQKVTVDCKQ YVCNGFQKC EQLLREYGQF CSKINQALHG ANLRQDDSVR NLFASVKSSQ SSPIIPGFGG DFNLTLLEPV SISTGSRSAR SAIEDLLFDK VTIADPGYM QGYDDCMQQG PASARDLICA QYVAGYKVLP PLMDVNMEAA YTSSLLGSIA GVGWTAGLSS FAAIPFAQSI F YRLNGVGI TQQVLSENQK LIANKFNQAL GAMQTGFTTT NEAFQKVQDA VNNNAQALSK LASELSNTFG AISASIGDII QR LDPPEQD AQIDRLINGR LTTLNAFVAQ QLVRSESAAL SAQLAKDKVN ECVKAQSKRS GFCGQGTHIV SFVVNAPNGL YFM HVGYYP SNHIEVVSAY GLCDAANPTN CIAPVNGYFI KTNNTRIVDE WSYTGSSFYA PEPITSLNTK YVAPQVTYQN ISTN LPPPL LGNSTGI

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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: 7.2
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: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 424874
FSC plot (resolution estimation)

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