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- EMDB-32686: Structure of NeoCOV RBD binding to Bat37 ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-32686
TitleStructure of NeoCOV RBD binding to Bat37 ACE2
Map data
Sample
  • Complex: NeoCOV RBD-Bat37 ACE2 complex
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / endocytosis involved in viral entry into host cell / cilium / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / endocytosis involved in viral entry into host cell / cilium / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / apical 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 / proteolysis / extracellular space / membrane / metal ion binding / cytoplasm
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 / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. ...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 / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesCoronavirus Neoromicia/PML-PHE1/RSA/2011 / Pipistrellus pipistrellus (common pipistrelle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCao L / Wang X / Tortorici MA / Veesler D
Funding support1 items
OrganizationGrant numberCountry
Not funded
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
DepositionJan 24, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32686.png

Downloads & links

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Map

FileDownload / File: emd_32686.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.67
Minimum - Maximum-2.022416 - 3.0346098
Average (Standard dev.)0.0045327772 (±0.09084825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NeoCOV RBD-Bat37 ACE2 complex

EntireName: NeoCOV RBD-Bat37 ACE2 complex
Components
  • Complex: NeoCOV RBD-Bat37 ACE2 complex
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: NeoCOV RBD-Bat37 ACE2 complex

SupramoleculeName: NeoCOV RBD-Bat37 ACE2 complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Coronavirus Neoromicia/PML-PHE1/RSA/2011

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Pipistrellus pipistrellus (common pipistrelle)
Molecular weightTheoretical: 80.775055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTEEEARDFL DKFNSEAENL SHESALASWD YNTNITDENA QKMNEADSKW SDFYKEQSKR AQAFPLQEIQ NLTIKLQLQI LQQNGSSVL TAEKSKRLST ILTTMSTIYS TGKVCNPNNP QQCFTLSGLE DIMEKSKDYH QRLWVWEGWR SEVGKQLRPL Y EEYVVLKN ...String:
TTEEEARDFL DKFNSEAENL SHESALASWD YNTNITDENA QKMNEADSKW SDFYKEQSKR AQAFPLQEIQ NLTIKLQLQI LQQNGSSVL TAEKSKRLST ILTTMSTIYS TGKVCNPNNP QQCFTLSGLE DIMEKSKDYH QRLWVWEGWR SEVGKQLRPL Y EEYVVLKN EMARGNNYED YGDYWRGDYE TEGEDGYNYS RNQLMEDVDR IFLEIKPLYE QLHAYVRAKL MNAYPSRISP TG CLPAHLL GDMWGRFWTN LYNLTVPFEQ KQNIDVTETM KKQSWDAEKI FKEAEKFYLS VGLYSMTQGF WNNSMLTEPS DGR QVVCHP TAWDLGEDDF RIKMCTKVTM DDFLTAHHEM GHIQYDMAYA KQPYLLRNGA NEGFHEAVGE VMSLSVATPK HLKG MGLLP SDFSEDNETE INFLLKQALN IVGTLPFTYM LEKWRWMVFE GKIPKEQWME KWWEMKREIV GVVEPLPHDE TYCDP ASLF HVANDYSFIR YFTRTILEFQ FQEALCKIAK HEGPLHKCDI SNSTEAGKKL KDMLELGKSK PWTYALNQIA RTKEMD AKP LLNYFEPLFS WLKKQNGNSV GWSADWSPYS EQSLKVRISL ISALGEKAYE WNDNEMYLFR SSVAYAMRVY FSKMNKT IP FTAEDVRVSD EKKRVSFKFF VTSPTNISDI IPRSEVEDAI RMSRSRINDA

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coronavirus Neoromicia/PML-PHE1/RSA/2011
Molecular weightTheoretical: 21.842541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AHVYPDCNFT ELFRERAPTI MQYKREVFTR CNYNLSLLLS LVQVDEFVCD KATPEALATG CYSSLTVDWF AFPYAWKSYL AIGSADRIV RFNYNQDYSN PSCRIHSKVN SSIGISYAGA YSYITNCNYG ATNKDDVVKP GGRASQQCIT GALNSPTTGQ L WAYNFGGV ...String:
AHVYPDCNFT ELFRERAPTI MQYKREVFTR CNYNLSLLLS LVQVDEFVCD KATPEALATG CYSSLTVDWF AFPYAWKSYL AIGSADRIV RFNYNQDYSN PSCRIHSKVN SSIGISYAGA YSYITNCNYG ATNKDDVVKP GGRASQQCIT GALNSPTTGQ L WAYNFGGV PYRVSRLTYT DHLSDPLDMV YVITVK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 5 / 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62545
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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