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- EMDB-30306: Structural basis for cross-species recognition of COVID-19 virus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30306
TitleStructural basis for cross-species recognition of COVID-19 virus spike receptor binding domain to bat ACE2
Map dataCryo-EM structure of bat ACE2
Sample
  • Cell: Bat ACE2
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsCOVID-19 / receptor binding domain (RBD) / Rhinolophus macrotis / PROTEIN BINDING
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / cilium / apical plasma membrane / proteolysis / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesBat AAV SC2991 (virus) / Rhinolophus macrotis (Big-eared Horseshoe Bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu KF / Wang J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cross-species recognition of SARS-CoV-2 to bat ACE2.
Authors: Kefang Liu / Shuguang Tan / Sheng Niu / Jia Wang / Lili Wu / Huan Sun / Yanfang Zhang / Xiaoqian Pan / Xiao Qu / Pei Du / Yumin Meng / Yunfei Jia / Qian Chen / Chuxia Deng / Jinghua Yan / ...Authors: Kefang Liu / Shuguang Tan / Sheng Niu / Jia Wang / Lili Wu / Huan Sun / Yanfang Zhang / Xiaoqian Pan / Xiao Qu / Pei Du / Yumin Meng / Yunfei Jia / Qian Chen / Chuxia Deng / Jinghua Yan / Hong-Wei Wang / Qihui Wang / Jianxun Qi / George Fu Gao /
Abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2- ...The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2-related coronaviruses have been isolated from bats and SARS-CoV-2 may infect bat, the structural basis for SARS-CoV-2 to utilize the human receptor counterpart bat angiotensin-converting enzyme 2 (bACE2) for virus infection remains less understood. Here, we report that the SARS-CoV-2 spike protein receptor binding domain (RBD) could bind to bACE2 from (bACE2-Rm) with substantially lower affinity compared with that to the human ACE2 (hACE2), and its infectivity to host cells expressing bACE2-Rm was confirmed with pseudotyped SARS-CoV-2 virus and SARS-CoV-2 wild virus. The structure of the SARS-CoV-2 RBD with the bACE2-Rm complex was determined, revealing a binding mode similar to that of hACE2. The analysis of binding details between SARS-CoV-2 RBD and bACE2-Rm revealed that the interacting network involving Y41 and E42 of bACE2-Rm showed substantial differences with that to hACE2. Bats have extensive species diversity and the residues for RBD binding in bACE2 receptor varied substantially among different bat species. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. These findings would benefit our understanding of the potential infection of SARS-CoV-2 in varied species of bats.
History
DepositionJun 2, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c8k
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30306.png

Downloads & links

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Map

FileDownload / File: emd_30306.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of bat ACE2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 160 pix.
= 159. Å		0.99 Å/pix.
x 160 pix.
= 159. Å		0.99 Å/pix.
x 160 pix.
= 159. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.023
Minimum - Maximum-0.04776762 - 0.10662766
Average (Standard dev.)0.00039786188 (±0.0039174003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 159.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.993750.993750.99375
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z159.000159.000159.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0480.1070.000

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Supplemental data

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Sample components

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Entire : Bat ACE2

EntireName: Bat ACE2
Components
  • Cell: Bat ACE2
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Bat ACE2

SupramoleculeName: Bat ACE2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bat AAV SC2991 (virus)

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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: Rhinolophus macrotis (Big-eared Horseshoe Bat)
Molecular weightTheoretical: 69.444312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEDEAKKF LDKFNSKAED LSYESSLASW DYNTNISDEN VQKMDEAGAK WSAFYEEQSK LAKNYPLEEI QNDTVKRQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCKPNN PQECLLLEPG LDNIMGTSKD YNERLWAWEG WRAEVGKQLR P LYEEYVVL ...String:
STTEDEAKKF LDKFNSKAED LSYESSLASW DYNTNISDEN VQKMDEAGAK WSAFYEEQSK LAKNYPLEEI QNDTVKRQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCKPNN PQECLLLEPG LDNIMGTSKD YNERLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARGYHY EDYGDYWRRD YETEESSGPG YSRDQLMKDV DRIFTEIKPL YEHLHAYVRA KLMDTYPLHI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD AMLNQGWDAN RIFKEAEKFF VSVSLPKMTE GFWNKSMLTE PGD GRKVVC HPTAWDLGKG DFRIKMCTKV TMEDFLTAHH EMGHIQYDMA YASQPYLLRN GANEGFHEAV GEVMSLSVAT PKHL KTMGL LSPDFREDDE TEINFLLKQA LNIVGTLPFT YMLEKWRWMV FKGEIPKEEW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVANDYSF IRYYTRTIFE FQFHEALCRI AQHNGPLHKC DISNSTDAGK KLHQMLSVGK SQAWTKTLED IVDSRN MDV GPLLRYFKPL YTWLQEQNRK SYVGWNTDWS PYA

UniProtKB: Angiotensin-converting enzyme

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

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62289
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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