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

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Basic information

Entry
Database: PDB / ID: 7bh9
TitleSARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRUS / In vitro evolution / Complex / receptor binding domain
Function / homology
Function and homology information


positive regulation of L-proline import across plasma membrane / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity ...positive regulation of L-proline import across plasma membrane / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity / regulation of vasoconstriction / blood vessel diameter maintenance / angiotensin maturation / carboxypeptidase activity / brush border membrane / metallocarboxypeptidase activity / regulation of cytokine production / negative regulation of signaling receptor activity / regulation of cardiac conduction / regulation of transmembrane transporter activity / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / metallopeptidase activity / viral translation / regulation of cell population proliferation / virus receptor activity / positive regulation of reactive oxygen species metabolic process / host cell surface receptor binding / endocytosis involved in viral entry into host cell / regulation of inflammatory response / endocytic vesicle membrane / endopeptidase activity / apical plasma membrane / viral protein processing / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / membrane raft / go:0009405: / proteolysis / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / integral component of membrane / extracellular region / identical protein binding / plasma membrane
Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Peptidase M2, peptidyl-dipeptidase A / Spike glycoprotein S2, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / in:ipr027400: / Collectrin domain / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein, betacoronavirus / Spike glycoprotein S2 superfamily, coronavirus ...Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Peptidase M2, peptidyl-dipeptidase A / Spike glycoprotein S2, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / in:ipr027400: / Collectrin domain / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein, betacoronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Angiotensin-converting enzyme
Spike glycoprotein / Angiotensin-converting enzyme 2
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsElad, N. / Dym, O. / Zahradnik, J. / Schreiber, G.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation3814/19 Israel
Israel Science Foundation1268/18 Israel
CitationJournal: To Be Published
Title: SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
Authors: Zahradnk, J. / Marciano, S. / Shemesh, M. / Zoler, E. / Chiaravalli, J. / Meyer, B. / Dym, O. / Elad, N. / Schreiber, G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

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Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2496
Polymers93,5202
Non-polymers7294
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2470 Å2
ΔGint-25 kcal/mol
Surface area32800 Å2
MethodPISA

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Components

#1: Protein Angiotensin-converting enzyme 2 / / Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related ...Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related carboxypeptidase / ACE-related carboxypeptidase / Metalloprotease MPROT15


Mass: 70486.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Homo sapiens (human)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Spike protein S1


Mass: 23033.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SARS-CoV-2 receptor binding domain
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domainCOMPLEX#1-#20RECOMBINANT
2ACE2 extracellular peptidase domainCOMPLEX#11RECOMBINANT
3SARS-CoV-2 receptor binding domainCOMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Buffer solutionpH: 7.2
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Calibrated magnification: 94518 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.214 sec. / Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4470

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.9image acquisition
4cryoSPARC3.0.1CTF correction
7PHENIXmodel fitting
9cryoSPARC3.0.1initial Euler assignment
10cryoSPARC3.0.1final Euler assignment
11cryoSPARC3.0.1classification
12cryoSPARC3.0.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164636 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6M0J
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076038
ELECTRON MICROSCOPYf_angle_d0.6738205
ELECTRON MICROSCOPYf_dihedral_angle_d9.0253508
ELECTRON MICROSCOPYf_chiral_restr0.047871
ELECTRON MICROSCOPYf_plane_restr0.0041050

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