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- EMDB-37701: Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with rab... -

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Basic information

Entry
Database: EMDB / ID: EMD-37701
TitleCryo-EM structure of SARS-CoV-2 prototype RBD in complex with rabbit ACE2 (local refinement)
Map dataSharp map of SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
Sample
  • Complex: SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsSARS-CoV-2 Omicron / receptor-binding domains (RBDs) / rabbit / angiotensin-converting enzyme 2 (ACE2) / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / negative regulation of signaling receptor activity ...Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / negative regulation of signaling receptor activity / brush border membrane / regulation of transmembrane transporter activity / cilium / metallopeptidase activity / virus receptor activity / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / identical protein binding / membrane / metal ion binding / plasma membrane / 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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...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, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / 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 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 speciesSevere acute respiratory syndrome coronavirus 2 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsLi LJ / Shi KY / Yu GH / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: mBio / Year: 2024
Title: Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Authors: Kaiyuan Shi / Linjie Li / Chunliang Luo / Zepeng Xu / Baihan Huang / Sufang Ma / Kefang Liu / Guanghui Yu / George F Gao /
Abstract: The potential host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been expanding alongside its evolution during the pandemic, with rabbits and hares being considered ...The potential host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been expanding alongside its evolution during the pandemic, with rabbits and hares being considered important potential hosts, supported by a report of rabbit sero-prevalence in nature. We measured the binding affinities of rabbit and hare angiotensin-converting enzyme 2 (ACE2) with receptor-binding domains (RBDs) from SARS-CoV, SARS-CoV-2, and its variants and found that rabbit and hare ACE2s had broad variant tropism, with significantly enhanced affinities to Omicron BA.4/5 and its subsequent-emerged sub-variants (>10 fold). The structures of rabbit ACE2 complexed with either SARS-CoV-2 prototype (PT) or Omicron BA.4/5 spike (S) proteins were determined, thereby unveiling the importance of rabbit ACE2 Q34 in RBD-interaction and elucidating the molecular basis of the enhanced binding with Omicron BA.4/5 RBD. These results address the highly enhanced risk of rabbits infecting SARS-CoV-2 Omicron sub-variants and the importance of constant surveillance.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has swept the globe and caused immense health and economic damage. SARS-CoV-2 has demonstrated a broad host range, indicating a high risk of interspecies transmission and adaptive mutation. Therefore, constant monitoring for potential hosts is of immense importance. In this study, we found that Omicron BA.4/5 and subsequent-emerged sub-variants exhibited enhanced binding to both rabbit and hare angiotensin-converting enzyme 2 (ACE2), and we elucidated the structural mechanism of their recognition. From the structure, we found that Q34, a unique residue of rabbit ACE2 compared to other ACE2 orthologs, plays an important role in ACE2 recognition. These results address the probability of rabbits/hares being potential hosts of SARS-CoV-2 and broaden our knowledge regarding the molecular mechanism of SARS-CoV-2 interspecies transmission.
History
DepositionOct 8, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37701.png

Downloads & links

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Map

FileDownload / File: emd_37701.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map of SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 480 pix.
= 422.4 Å		0.88 Å/pix.
x 480 pix.
= 422.4 Å		0.88 Å/pix.
x 480 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.0017219365 - 2.7376487
Average (Standard dev.)0.00035982174 (±0.01272048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A map of SARS-CoV-2 prototype spike protein...

Fileemd_37701_half_map_1.map
AnnotationHalf A map of SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of SARS-CoV-2 prototype spike protein...

Fileemd_37701_half_map_2.map
AnnotationHalf B map of SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (l...

EntireName: SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
Components
  • Complex: SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (l...

SupramoleculeName: SARS-CoV-2 prototype spike protein in complex with rabbit ACE2 (local refined)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.951219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFHHHHH H

UniProtKB: Spike glycoprotein

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Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 69.017414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: STIEELAKTF LEKFNQEAED LSYQSALASW DYNTNITEEN VQKMNDAEAK WSAFYEEQSK LAKTYPSQEV QNLTVKRQLQ ALQQSGSSA LSADKSKQLN TILSTMSTIY STGKVCNQSN PQECFLLEPG LDEIMAKSTD YNERLWAWEG WRSVVGKQLR P LYEEYVVL ...String:
STIEELAKTF LEKFNQEAED LSYQSALASW DYNTNITEEN VQKMNDAEAK WSAFYEEQSK LAKTYPSQEV QNLTVKRQLQ ALQQSGSSA LSADKSKQLN TILSTMSTIY STGKVCNQSN PQECFLLEPG LDEIMAKSTD YNERLWAWEG WRSVVGKQLR P LYEEYVVL KNEMARANNY EDYGDYWRAD YEAEGADGYD YSRSQLIDDV ERTFSEIKPL YEQLHAFVRT KLMDAYPSRI SP TGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD TMVNQGWDAE RIFKEAEKFF VSVGLPSMTQ GFWENSMLTE PGD GRKVVC HPTAWDLGKG DFRIKMCTKV TMDNFLTAHH EMGHIQYDMA YATQPFLLRN GANEGFHEAV GEIMSLSAAT PEHL KSIGL LPYDFHEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKEQW MQKWWEMKRE IVGVVEPMPH DETYC DPAA LFHVANDYSF IRYYTRTIYQ FQFQEALCQA AQHEGPLHKC DISNSTEAGQ KLLNMLRLGR SEPWTLALEN VVGAKN MDV RPLLNYFEPL FTWLKEQNRN SFVGWSTEWT 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: 1 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 350247
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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