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- EMDB-12187: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain -

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Basic information

Entry
Database: EMDB / ID: EMD-12187
TitleSARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Map dataSARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Sample
  • Complex: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
    • Complex: ACE2 extracellular peptidase domain
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / endopeptidase activity / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / 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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / membrane raft / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / 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 / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsElad N / Dym O / Zahradnik J / Schreiber G
Funding support Israel, 2 items
OrganizationGrant numberCountry
Israel Science Foundation3814/19 Israel
Israel Science Foundation1268/18 Israel
CitationJournal: Nat Microbiol / Year: 2021
Title: SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution.
Authors: Jiří Zahradník / Shir Marciano / Maya Shemesh / Eyal Zoler / Daniel Harari / Jeanne Chiaravalli / Björn Meyer / Yinon Rudich / Chunlin Li / Ira Marton / Orly Dym / Nadav Elad / Mark G ...Authors: Jiří Zahradník / Shir Marciano / Maya Shemesh / Eyal Zoler / Daniel Harari / Jeanne Chiaravalli / Björn Meyer / Yinon Rudich / Chunlin Li / Ira Marton / Orly Dym / Nadav Elad / Mark G Lewis / Hanne Andersen / Matthew Gagne / Robert A Seder / Daniel C Douek / Gideon Schreiber /
Abstract: SARS-CoV-2 variants of interest and concern will continue to emerge for the duration of the COVID-19 pandemic. To map mutations in the receptor-binding domain (RBD) of the spike protein that affect ...SARS-CoV-2 variants of interest and concern will continue to emerge for the duration of the COVID-19 pandemic. To map mutations in the receptor-binding domain (RBD) of the spike protein that affect binding to angiotensin-converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, we applied in vitro evolution to affinity-mature the RBD. Multiple rounds of random mutagenic libraries of the RBD were sorted against decreasing concentrations of ACE2, resulting in the selection of higher affinity RBD binders. We found that mutations present in more transmissible viruses (S477N, E484K and N501Y) were preferentially selected in our high-throughput screen. Evolved RBD mutants include prominently the amino acid substitutions found in the RBDs of B.1.620, B.1.1.7 (Alpha), B1.351 (Beta) and P.1 (Gamma) variants. Moreover, the incidence of RBD mutations in the population as presented in the GISAID database (April 2021) is positively correlated with increased binding affinity to ACE2. Further in vitro evolution increased binding by 1,000-fold and identified mutations that may be more infectious if they evolve in the circulating viral population, for example, Q498R is epistatic to N501Y. We show that our high-affinity variant RBD-62 can be used as a drug to inhibit infection with SARS-CoV-2 and variants Alpha, Beta and Gamma in vitro. In a model of SARS-CoV-2 challenge in hamster, RBD-62 significantly reduced clinical disease when administered before or after infection. A 2.9 Å cryo-electron microscopy structure of the high-affinity complex of RBD-62 and ACE2, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies.
History
DepositionJan 11, 2021-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateSep 22, 2021-
Current statusSep 22, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.2
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  • Surface view with fitted model
  • Atomic models: PDB-7bh9
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12187.png

Downloads & links

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Map

FileDownload / File: emd_12187.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Voxel sizeX=Y=Z: 0.529 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.46074307 - 1.033728
Average (Standard dev.)-0.00020314161 (±0.037162308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin170170170
Dimensions340340340
Spacing340340340
CellA=B=C: 179.86 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5290.5290.529
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z179.860179.860179.860
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS170170170
NC/NR/NS340340340
D min/max/mean-0.4611.034-0.000

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Supplemental data

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Additional map: Sharpened map, B-factor of -83

Fileemd_12187_additional_1.map
AnnotationSharpened map, B-factor of -83
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12187_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12187_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain

EntireName: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Components
  • Complex: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
    • Complex: ACE2 extracellular peptidase domain
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain

SupramoleculeName: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: ACE2 extracellular peptidase domain

SupramoleculeName: ACE2 extracellular peptidase domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: SARS-CoV-2 receptor binding domain

SupramoleculeName: SARS-CoV-2 receptor binding domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.486039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSSTIEEQAK TFLDKFNHEA EDLFYQSSLA SWNYNTNITE ENVQNMNNAG DKWSAFLKEQ STLAQMYPLQ EIQNLTVKLQ LQALQQNGS SVLSEDKSKR LNTILNTMST IYSTGKVCNP DNPQECLLLE PGLNEIMANS LDYNERLWAW ESWRSEVGKQ L RPLYEEYV ...String:
GSSTIEEQAK TFLDKFNHEA EDLFYQSSLA SWNYNTNITE ENVQNMNNAG DKWSAFLKEQ STLAQMYPLQ EIQNLTVKLQ LQALQQNGS SVLSEDKSKR LNTILNTMST IYSTGKVCNP DNPQECLLLE PGLNEIMANS LDYNERLWAW ESWRSEVGKQ L RPLYEEYV VLKNEMARAN HYEDYGDYWR GDYEVNGVDG YDYSRGQLIE DVEHTFEEIK PLYEHLHAYV RAKLMNAYPS YI SPIGCLP AHLLGDMWGR FWTNLYSLTV PFGQKPNIDV TDAMVDQAWD AQRIFKEAEK FFVSVGLPNM TQGFWENSML TDP GNVQKA VCHPTAWDLG KGDFRILMCT KVTMDDFLTA HHEMGHIQYD MAYAAQPFLL RNGANEGFHE AVGEIMSLSA ATPK HLKSI GLLSPDFQED NETEINFLLK QALTIVGTLP FTYMLEKWRW MVFKGEIPKD QWMKKWWEMK REIVGVVEPV PHDET YCDP ASLFHVSNDY SFIRYYTRTL YQFQFQEALC QAAKHEGPLH KCDISNSTEA GQKLFNMLRL GKSEPWTLAL ENVVGA KNM NVRPLLNYFE PLFTWLKDQN KNSFVGWSTD WSPYADGGSG THHHHHH

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Details: SARS-CoV-2 receptor binding domain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 23.033965 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRFSNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKKGGNYNY LYRLFRKSKL KPFERDTSME IYQAGNTPCN GVKGFNCYFP L QSYGFRPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRFSNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKKGGNYNY LYRLFRKSKL KPFERDTSME IYQAGNTPCN GVKGFNCYFP L QSYGFRPT YGVGYQPYRV VVLSFELLHA PATVCGPKHH HHHH

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / 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

Concentration3.5 mg/mL
BufferpH: 7.2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 94518 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 4470 / Average exposure time: 1.214 sec. / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.0.1)
Startup modelType of model: INSILICO MODEL / Details: phenix.dock_in_map
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.1) / Number images used: 164636
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6m0j

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7bh9:
SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain

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