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- EMDB-40979: Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 tri... -

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Entry
Database: EMDB / ID: EMD-40979
TitleCryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement at upRBD conformation
Map dataCryo-EM Map of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement
Sample
  • Complex: mink variant spike RBD-ACE2 interface after local refinement
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCoronavirus / Spike / ACE2 / Mink / PROTEIN BINDING / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus 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 / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Neovison vison (American mink) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsAhn HM / Calderon B / Fan X / Gao Y / Horgan N / Zhou B / Liang B
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: J Med Virol / Year: 2023
Title: Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS-CoV-2.
Authors: Hyunjun Ahn / Brenda M Calderon / Xiaoyu Fan / Yunrong Gao / Natalie L Horgan / Nannan Jiang / Dylan S Blohm / Jaber Hossain / Nicole Wedad K Rayyan / Sarah H Osman / Xudong Lin / Michael ...Authors: Hyunjun Ahn / Brenda M Calderon / Xiaoyu Fan / Yunrong Gao / Natalie L Horgan / Nannan Jiang / Dylan S Blohm / Jaber Hossain / Nicole Wedad K Rayyan / Sarah H Osman / Xudong Lin / Michael Currier / John Steel / David E Wentworth / Bin Zhou / Bo Liang /
Abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across ...Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS-CoV-2 viruses impact species specificity. Reverse zoonoses led to SARS-CoV-2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink-associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio-layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink-derived S glycoproteins of SARS-CoV-2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo-electron microscopy (cryo-EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor-binding domain (RBD) of the S glycoprotein in a "down" position, approximately 34° lower than previously reported "up" RBD. Finally, we compared residue interactions in the S-ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS-CoV-2 entry.
History
DepositionJun 5, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40979.png

Downloads & links

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Map

FileDownload / File: emd_40979.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM Map of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 512 pix.
= 568.32 Å		1.11 Å/pix.
x 512 pix.
= 568.32 Å		1.11 Å/pix.
x 512 pix.
= 568.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.0985396 - 2.2432556
Average (Standard dev.)-0.0008392595 (±0.019448891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of the density of the RBD-ACE2...

Fileemd_40979_half_map_1.map
AnnotationHalf map of the density of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the density of the RBD-ACE2...

Fileemd_40979_half_map_2.map
AnnotationHalf map of the density of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mink variant spike RBD-ACE2 interface after local refinement

EntireName: mink variant spike RBD-ACE2 interface after local refinement
Components
  • Complex: mink variant spike RBD-ACE2 interface after local refinement
    • 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: mink variant spike RBD-ACE2 interface after local refinement

SupramoleculeName: mink variant spike RBD-ACE2 interface after local refinement
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: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neovison vison (American mink)
Molecular weightTheoretical: 89.3755 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGSSWLLLS LAALTAAQST TEDLAKTFLE KFNYEAEELS YQNSLASWNY NTNITDENIQ KMNIAGAKWS AFYEEESQHA KTYPLEEIQ DPIIKRQLRA LQQSGSSVLS ADKRERLNTI LNAMSTIYST GKACNPNNPQ ECLLLEPGLD DIMENSKDYN E RLWAWEGW ...String:
MLGSSWLLLS LAALTAAQST TEDLAKTFLE KFNYEAEELS YQNSLASWNY NTNITDENIQ KMNIAGAKWS AFYEEESQHA KTYPLEEIQ DPIIKRQLRA LQQSGSSVLS ADKRERLNTI LNAMSTIYST GKACNPNNPQ ECLLLEPGLD DIMENSKDYN E RLWAWEGW RSEVGKQLRP LYEEYVALKN EMARANNYED YGDYWRGDYE EEWADGYNYS RNQLIEDVEH TFTQIKPLYE HL HAYVRAK LMDAYPSRIS PTGCLPAHLL GDMWGRFWTN LYPLMVPFGQ KPNIDVTDAM VNQSWDARRI FKEAEKFFVS VGL PNMTEG FWQNSMLTEP GDNRKVVCHP TAWDLGKHDF RIKMCTKVTM DDFLTAHHEM GHIQYDMAYA AQPFLLRNGA NEGF HEAVG EIMSLSAATP NHLKNIGLLP PDFSEDSETD INFLLKQALT IVGTLPFTYM LEKWRWMVFK GEIPKEQWMQ KWWEM KRDI VGVVEPLPHD ETYCDPAALF HVANDYSFIR YYTRTIYQFQ FQEALCQIAK HEGPLYKCDI SNSREAGQKL HEMLSL GRS KPWTFALERV VGAKTMDVRP LLNYFEPLFT WLKEQNRNSF VGWNTDWSPY ADQSIKVRIS LKSALGEKAY EWNDNEM YF FQSSIAYAMR EYFSKVKKQT IPFVDKDVRV SDLKPRISFN FIVTSPENMS DIIPRADVEE AIRKSRGRIN DAFRLDDN S LEFLGIQPTL EPPYQPPVGS GSGSGHHHHH HGSGSGLNDI FEAQKIEWHE

UniProtKB: Angiotensin-converting enzyme

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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: Homo sapiens (human)
Molecular weightTheoretical: 23.370246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQ IAPGQTGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLFRLFRKS NLKPFERDIS TEIYQAGSTP C NGVEGFNC ...String:
QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQ IAPGQTGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLFRLFRKS NLKPFERDIS TEIYQAGSTP C NGVEGFNC YFPLQSYGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris Buffer
200.0 mMNaClSodium Chloride

Details: 20 mM Tris pH 8.0, 200 mM NaCl
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 11392 / Average exposure time: 4.0 sec. / Average electron dose: 49.98 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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:

7f5r

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 512722
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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