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Basic information

Entry
Database: PDB / ID: 7rpv
TitleCrystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsHydrolase/Viral protein / SARS-CoV-2 / receptor binding domain / engineered human ACE2 / enhanced affinity / catalytic-null / zinc binding site / Hydrolase-Viral protein complex
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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
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. / 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 / 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. / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsChen, Y. / Tolbert, D.W. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentStart-up funds from the Uniformed Services University of the Health Sciences United States
CitationJournal: Biorxiv / Year: 2021
Title: Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities.
Authors: Chen, Y. / Sun, L. / Ullah, I. / Beaudoin-Bussieres, G. / Anand, S.P. / Hederman, A.P. / Tolbert, W.D. / Sherburn, R. / Nguyen, D.N. / Marchitto, L. / Ding, S. / Wu, D. / Luo, Y. / ...Authors: Chen, Y. / Sun, L. / Ullah, I. / Beaudoin-Bussieres, G. / Anand, S.P. / Hederman, A.P. / Tolbert, W.D. / Sherburn, R. / Nguyen, D.N. / Marchitto, L. / Ding, S. / Wu, D. / Luo, Y. / Gottumukkala, S. / Moran, S. / Kumar, P. / Piszczek, G. / Mothes, W. / Ackerman, M.E. / Finzi, A. / Uchil, P.D. / Gonzalez, F.J. / Pazgier, M.
History
DepositionAug 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
E: Spike protein S1
B: Processed angiotensin-converting enzyme 2
F: Spike protein S1
C: Processed angiotensin-converting enzyme 2
G: Spike protein S1
D: Processed angiotensin-converting enzyme 2
H: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,05936
Polymers374,4898
Non-polymers5,57128
Water543
1
A: Processed angiotensin-converting enzyme 2
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0159
Polymers93,6222
Non-polymers1,3937
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Processed angiotensin-converting enzyme 2
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0159
Polymers93,6222
Non-polymers1,3937
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Processed angiotensin-converting enzyme 2
G: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0159
Polymers93,6222
Non-polymers1,3937
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Processed angiotensin-converting enzyme 2
H: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0159
Polymers93,6222
Non-polymers1,3937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.666, 136.307, 132.673
Angle α, β, γ (deg.)90.000, 92.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Processed angiotensin-converting enzyme 2


Mass: 69120.570 Da / Num. of mol.: 4
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
#2: Protein
Spike protein S1


Mass: 24501.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: 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.: 24 / 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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES pH6.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.54→50 Å / Num. obs: 56056 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 108.37 Å2 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.14 / Rrim(I) all: 0.262 / Χ2: 1.128 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.54-3.6131.3327710.4470.8961.6111.10296.8
3.61-3.683.11.14627670.5740.7591.3811.08597
3.68-3.753.20.9827390.6230.6441.1771.10896.7
3.75-3.823.20.73328010.7610.4780.8791.12897.5
3.82-3.913.20.72628000.7090.4720.871.14697.9
3.91-43.20.64127690.650.4270.7741.0697.6
4-4.13.10.63126400.7310.4210.7631.11192.1
4.1-4.213.20.49827040.8530.3210.5951.12195
4.21-4.333.60.43128500.880.2660.5071.14999.4
4.33-4.473.60.34228150.9070.210.4021.07799.2
4.47-4.633.60.30928390.9520.1890.3631.18199.4
4.63-4.823.60.29128550.9290.180.3431.11399.3
4.82-5.043.50.28828670.9280.1780.341.11799.4
5.04-5.33.50.24928510.940.1550.2941.11199.4
5.3-5.633.40.23828270.9450.1510.2831.08599
5.63-6.073.20.21927270.9470.1450.2641.0994.9
6.07-6.683.50.19128120.9610.1180.2251.06897.9
6.68-7.643.60.12728920.980.0770.1491.06199.3
7.64-9.613.50.07328630.9920.0450.0861.05299.2
9.61-503.40.05328670.940.0350.0641.57196.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R4L, 6M0J

1r4l

6m0j


Resolution: 3.54→47.92 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 2659 4.75 %
Rwork0.2435 53286 -
obs0.2457 55945 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 300.57 Å2 / Biso mean: 122.788 Å2 / Biso min: 33.86 Å2
Refinement stepCycle: final / Resolution: 3.54→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25345 0 340 3 25688
Biso mean--126.05 37.15 -
Num. residues----3125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.54-3.60.3861190.36872430254983
3.6-3.670.42081430.35142756289997
3.67-3.750.36111370.33352771290896
3.75-3.830.35031560.31372801295797
3.83-3.920.36081600.31382800296098
3.92-4.010.35831840.29482762294697
4.01-4.120.36491250.29532612273791
4.12-4.240.24341210.26962846296798
4.24-4.380.27741270.24892880300799
4.38-4.540.31641490.22622851300099
4.54-4.720.27941600.24132861302199
4.72-4.930.30281390.24072864300399
4.93-5.190.31611180.240428963014100
5.19-5.520.28761560.23092873302999
5.52-5.940.30781420.25232857299998
5.94-6.540.27541170.26042756287395
6.54-7.480.24381600.23342866302699
7.49-9.420.21381290.18572928305799
9.42-47.920.23821170.1812876299395

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