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- PDB-7pki: Crystal structure of human ACE2 bound to the spike receptor-bindi... -

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Basic information

Entry
Database: PDB / ID: 7pki
TitleCrystal structure of human ACE2 bound to the spike receptor-binding domain from a cave bat sarbecovirus closely related to SARS-CoV-2.
Components
  • BANAL 236 coronavirus spike receptor-binding domain
  • Processed angiotensin-converting enzyme 2
KeywordsVIRAL PROTEIN / Coronavirus / receptor binding domain / human ACE2.
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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / 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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / 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 / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / 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.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Sarbecovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94234133444 Å
AuthorsBaquero, E. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur InstituteAlloSpike France
CitationJournal: Nature / Year: 2022
Title: Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.
Authors: Temmam, S. / Vongphayloth, K. / Baquero, E. / Munier, S. / Bonomi, M. / Regnault, B. / Douangboubpha, B. / Karami, Y. / Chretien, D. / Sanamxay, D. / Xayaphet, V. / Paphaphanh, P. / Lacoste, ...Authors: Temmam, S. / Vongphayloth, K. / Baquero, E. / Munier, S. / Bonomi, M. / Regnault, B. / Douangboubpha, B. / Karami, Y. / Chretien, D. / Sanamxay, D. / Xayaphet, V. / Paphaphanh, P. / Lacoste, V. / Somlor, S. / Lakeomany, K. / Phommavanh, N. / Perot, P. / Dehan, O. / Amara, F. / Donati, F. / Bigot, T. / Nilges, M. / Rey, F.A. / van der Werf, S. / Brey, P.T. / Eloit, M.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
E: BANAL 236 coronavirus spike receptor-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,11823
Polymers91,1012
Non-polymers3,01721
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex isolated by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-53 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)341.535, 341.535, 68.153
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11E-1801-

HOH

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Components

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Protein , 2 types, 2 molecules AE

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 69038.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Plasmid: pcDNA3.1(+) / Cell line (production host): Expi293 GnTI / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1
#2: Protein BANAL 236 coronavirus spike receptor-binding domain


Mass: 22062.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sarbecovirus / Strain: BANAL 236 / Gene: Spike / Plasmid: pCAGGS / Cell line (production host): Espi293 GnTI / Production host: Homo sapiens (human)

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Sugars , 2 types, 7 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
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

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Non-polymers , 7 types, 22 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.17 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris 8.5, 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.942→49.63 Å / Num. obs: 43645 / % possible obs: 86.98 % / Redundancy: 2 % / Biso Wilson estimate: 68.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.42
Reflection shellResolution: 2.942→3.047 Å / Rmerge(I) obs: 4.562 / Num. unique obs: 614 / CC1/2: 0.496

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
autoBUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 2.94234133444→49.2963310469 Å / SU ML: 0.293331497159 / Cross valid method: FREE R-VALUE / σ(F): 1.34352455118 / Phase error: 25.2228022368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227196056333 2169 4.97078033689 %
Rwork0.214370371042 41466 -
obs0.21501689136 43635 87.0193841736 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.6809885402 Å2
Refinement stepCycle: LAST / Resolution: 2.94234133444→49.2963310469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6418 0 184 8 6610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005021972165936784
X-RAY DIFFRACTIONf_angle_d0.8799746446499224
X-RAY DIFFRACTIONf_chiral_restr0.0436209670625981
X-RAY DIFFRACTIONf_plane_restr0.004549242857991178
X-RAY DIFFRACTIONf_dihedral_angle_d14.31487132883964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94234133444-3.01080.516725065049150.306890915889253X-RAY DIFFRACTION8.23348694316
3.0108-3.08610.303038482274510.3363030576391033X-RAY DIFFRACTION32.6998491704
3.0861-3.16950.3211731692931150.3305945357642258X-RAY DIFFRACTION72.7690892364
3.1695-3.26270.3444320673991420.3253333721952827X-RAY DIFFRACTION89.7249924448
3.2627-3.3680.3230403862661590.3042841021343061X-RAY DIFFRACTION98.5312117503
3.368-3.48840.286711013741900.2919432213973104X-RAY DIFFRACTION100
3.4884-3.6280.3112874641541640.2673673940423158X-RAY DIFFRACTION99.9699067108
3.628-3.79310.2775486313941620.2460220823883175X-RAY DIFFRACTION100
3.7931-3.99290.2175406070851720.2199386947343134X-RAY DIFFRACTION100
3.9929-4.2430.2007419557481270.1997359048463197X-RAY DIFFRACTION100
4.243-4.57040.2047568249211550.1776720122153191X-RAY DIFFRACTION100
4.5704-5.02990.1773420466031780.1663444749873165X-RAY DIFFRACTION100
5.0299-5.75680.2102745249651710.1796738056643230X-RAY DIFFRACTION100
5.7568-7.24930.2155565790321800.1997264202523242X-RAY DIFFRACTION100
7.2493-49.29633104690.1710659487041880.1737618223233438X-RAY DIFFRACTION99.779856907

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