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- EMDB-26378: Cryo-EM structure of PDF-2180 Spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-26378
TitleCryo-EM structure of PDF-2180 Spike glycoprotein
Map dataSharpen map
Sample
  • Virus: PREDICT/PDF-2180 (virus)
    • Protein or peptide: PDF-2180 Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / 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-like / 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 speciesBat coronavirus / PREDICT/PDF-2180 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsTortorici MA / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2022
Title: Close relatives of MERS-CoV in bats use ACE2 as their functional receptors.
Authors: Qing Xiong / Lei Cao / Chengbao Ma / M Alejandra Tortorici / Chen Liu / Junyu Si / Peng Liu / Mengxue Gu / Alexandra C Walls / Chunli Wang / Lulu Shi / Fei Tong / Meiling Huang / Jing Li / ...Authors: Qing Xiong / Lei Cao / Chengbao Ma / M Alejandra Tortorici / Chen Liu / Junyu Si / Peng Liu / Mengxue Gu / Alexandra C Walls / Chunli Wang / Lulu Shi / Fei Tong / Meiling Huang / Jing Li / Chufeng Zhao / Chao Shen / Yu Chen / Huabin Zhao / Ke Lan / Davide Corti / David Veesler / Xiangxi Wang / Huan Yan /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) and several bat coronaviruses use dipeptidyl peptidase-4 (DPP4) as an entry receptor. However, the receptor for NeoCoV-the closest known MERS- ...Middle East respiratory syndrome coronavirus (MERS-CoV) and several bat coronaviruses use dipeptidyl peptidase-4 (DPP4) as an entry receptor. However, the receptor for NeoCoV-the closest known MERS-CoV relative found in bats-remains unclear. Here, using a pseudotype virus entry assay, we found that NeoCoV and its close relative, PDF-2180, can efficiently bind to and use specific bat angiotensin-converting enzyme 2 (ACE2) orthologues and, less favourably, human ACE2 as entry receptors through their receptor-binding domains (RBDs) on the spike (S) proteins. Cryo-electron microscopy analysis revealed an RBD-ACE2 binding interface involving protein-glycan interactions, distinct from those of other known ACE2-using coronaviruses. We identified residues 337-342 of human ACE2 as a molecular determinant restricting NeoCoV entry, whereas a NeoCoV S pseudotyped virus containing a T510F RBD mutation efficiently entered cells expressing human ACE2. Although polyclonal SARS-CoV-2 antibodies or MERS-CoV RBD-specific nanobodies did not cross-neutralize NeoCoV or PDF-2180, an ACE2-specific antibody and two broadly neutralizing betacoronavirus antibodies efficiently inhibited these two pseudotyped viruses. We describe MERS-CoV-related viruses that use ACE2 as an entry receptor, underscoring a promiscuity of receptor use and a potential zoonotic threat.
History
DepositionMar 5, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26378.png

Downloads & links

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Map

FileDownload / File: emd_26378.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpen map
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy EMDB: 1.5
Minimum - Maximum-5.0109167 - 8.746828
Average (Standard dev.)0.0014133997 (±0.19110686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_26378_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map

Fileemd_26378_half_map_1.map
AnnotationHalf_B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map

Fileemd_26378_half_map_2.map
AnnotationHalf_A 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 : PREDICT/PDF-2180

EntireName: PREDICT/PDF-2180 (virus)
Components
  • Virus: PREDICT/PDF-2180 (virus)
    • Protein or peptide: PDF-2180 Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PREDICT/PDF-2180

SupramoleculeName: PREDICT/PDF-2180 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2042537 / Sci species name: PREDICT/PDF-2180 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Pipistrellus cf. hesperidus

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Macromolecule #1: PDF-2180 Spike glycoprotein

MacromoleculeName: PDF-2180 Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bat coronavirus
Molecular weightTheoretical: 147.475578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTYSVSLLMC LLTFIGANAK IVSIPGGVGT GACPQVDMQP SYFIKHNWPE PIDMNKADGV IYPNGRTYSN ITLQTTNLFP RNGDLGTQY VYSASNEKSR TSNVAFISNY SYYGNPFGDG IVIRIGQNSN KTGSVIVGTA QTTIKKIYPA LMLGSSFGNF S VNNKSGAY ...String:
MTYSVSLLMC LLTFIGANAK IVSIPGGVGT GACPQVDMQP SYFIKHNWPE PIDMNKADGV IYPNGRTYSN ITLQTTNLFP RNGDLGTQY VYSASNEKSR TSNVAFISNY SYYGNPFGDG IVIRIGQNSN KTGSVIVGTA QTTIKKIYPA LMLGSSFGNF S VNNKSGAY FNHTLLILPS KCGTVFQVAY CLLQPRTDSY CPGNANYVSY ALIDSPTDCT SADESKRRNG LEDIKKYFNL VN CTYFEEF NVTADERAEW FGITQDSQGV HLYTSRKNGF NSNNLFLFAS VPIYDKINYY TVIPRSIITP ANQRSAWAAF YVY PLHQLS YLLNFDVNGY ITQAADCGYN DYTQLVCSYG DFNMKSGVYS TSYYSAKPVG AYYEAHVYPD CNFTDLFREN APTI MQYKR QVFTRCNYNL TLLLSLVQVD EFVCDKITPE ALATGCYSSL TVDWFAFPYA WKSYLAIGSA DRIVRFNYNQ DYSNP SCRI HSKVNSSVGI SYSGLYSYIT NCNYGGFNKD DVVKPGGRAS QPCVTGALNS PTNGQVWSFN FGGVPYRTSR LTYTDH LKN PLDMVYVITV KYEPGAETVC PKQVRPDYST NITGLLGSCI SYDIYGITGT GVFQLCNATG IPQQKFVYDK FDNIIGF HS DDGNYYCVAP CVSVPVSVIY DDNTNQYATL FGSVACQHIS TMAAQFSRET RASLVSRNMQ NLLQTSVGCV MGFHETND T VEDCNLSLGQ SLCAIPPNTN LRVGRSTFGL GSLAYNSPLR VDALNSSEFK VSLPLNFTFG VTQEYIETSI QKITVDCKQ YVCNGFAKCE KLLEQYGQFC SKINQALHGA NLRQDDFVRN LFESVKTPQT VPLTTGFGGE FNLTLLEPLS VSTGSSNARS ALEELLFDK VTIADPGYMQ GYDDCMQQGP ASARDLICAQ YVAGYKVLPP LMDVNMEAAY TSSLLGSIAG AGWTAGLSSF A AIPFAQSI FYRLNGVGIT QQVLSENQKI IANKFNQALG AMQTGFTTTN EAFQKVQDAV NTNAQALAKL ASELSNTFGA IS SSIGDII QRLDVLEQEV QIDRLINGRL TTLNAFVAQQ LVRSESAARS AQLAKDKVNE CVKSQSTRSG FCGQGTHIVS FVI NAPNGL YFMHVGYHPS QHIEVVAAYG LCDAANPTNC IAPVNGYFIK NQTTRGVDDW SYTGSSFYAP EPITTLNTRY VAPQ VTFQN ISTNLPPPLL GNSTGTDFKD ELDEFFKNVS TSIPNFGALT QINTTLLDLS DEMLALQQVV KALNESYIDL KELGN YTYY NKGSGRENLY FQGGGGSGYI PEAPRDGQAY VRKDGEWVLL STFLGHHHHH HHH

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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: 39 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Sugar embeddingMaterial: Tris buffer saline
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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5w9j

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47094
FSC plot (resolution estimation)

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