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- PDB-7vib: Crystal structure of human ACE2 and GX/P2V RBD -

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Basic information

Entry
Database: PDB / ID: 7vib
TitleCrystal structure of human ACE2 and GX/P2V RBD
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / HYDROLASE
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 / viral translation / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / 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 / 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, 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. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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)
Pangolin coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGuo, Y. / Cao, W. / Jia, N. / Wang, W. / Yuan, S. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670731 China
National Natural Science Foundation of China (NSFC)31870733 China
CitationJournal: To Be Published
Title: Crystal structure of human ACE2 and GX/P2V RBD
Authors: Guo, Y. / Cao, W. / Jia, N. / Wang, W. / Yuan, S. / Wang, Y.
History
DepositionSep 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
B: Spike glycoprotein
C: Angiotensin-converting enzyme 2
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,8396
Polymers181,7084
Non-polymers1312
Water00
1
A: Angiotensin-converting enzyme 2
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9193
Polymers90,8542
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-43 kcal/mol
Surface area33920 Å2
MethodPISA
2
C: Angiotensin-converting enzyme 2
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9193
Polymers90,8542
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-41 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.672, 120.150, 107.885
Angle α, β, γ (deg.)90.000, 96.610, 90.000
Int Tables number4
Space group name H-MP1211

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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: 69153.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: unidentified baculovirus
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 21700.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pangolin coronavirus / Production host: unidentified baculovirus / References: UniProt: A0A6G6A2Q2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) PEG3000 100 mM CAPS pH10.5 200 mM Nacl 10 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 50664 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.064 / Rrim(I) all: 0.125 / Χ2: 0.634 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.2640.71317130.7560.4170.8290.6599.9
3.26-3.3140.62516520.8040.3640.7260.605100
3.31-3.3840.5617260.8150.3270.6510.61199.9
3.38-3.453.20.46216210.9320.3070.5580.97295.4
3.45-3.523.40.38315960.8950.2430.4560.66396
3.52-3.63.90.30516700.9320.1810.3560.60799.6
3.6-3.693.40.31416390.8730.2010.3751.00695.6
3.69-3.7940.23816750.9580.1370.2750.62999.7
3.79-3.913.50.20916040.9060.1320.2490.92194.5
3.91-4.033.50.15716170.9640.0950.1850.59893.5
4.03-4.183.80.13616650.9710.0810.1590.60999.5
4.18-4.343.60.11516900.9760.070.1350.60799.6
4.34-4.543.90.09117030.9860.0530.1060.57799.6
4.54-4.783.90.08316910.9860.0480.0960.58999.5
4.78-5.083.80.07316870.9910.0430.0850.58699.5
5.08-5.473.60.06617040.9870.040.0770.5299.4
5.47-6.0240.06417060.9880.0370.0740.49999.8
6.02-6.893.90.0517060.9860.0290.0580.49599.9
6.89-8.673.70.02817120.9940.0170.0330.50599.7
8.67-503.50.02117320.9880.0130.0250.6497.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.2→47.29 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 3295 6.5 %
Rwork0.2036 47369 -
obs0.2072 50664 75.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.94 Å2 / Biso mean: 60.0022 Å2 / Biso min: 35.58 Å2
Refinement stepCycle: final / Resolution: 3.2→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12685 0 2 0 12687
Biso mean--76.79 --
Num. residues----1566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.250.3273400.306961365323
3.25-3.30.369610.274392298335
3.3-3.350.2985710.3025995106639
3.35-3.40.3369780.2951211128946
3.4-3.460.3966720.3281006107839
3.46-3.530.3353950.29161390148553
3.53-3.590.32861100.25631691180165
3.59-3.670.35811190.26731733185266
3.67-3.750.26671320.27831863199571
3.75-3.830.27931540.23612115226982
3.83-3.930.35251330.26431778191168
3.93-4.030.26871500.21682187233783
4.04-4.150.28611670.21152334250190
4.15-4.290.30071690.21112455262493
4.29-4.440.26591720.1942464263696
4.44-4.620.22381800.17782551273197
4.62-4.830.21641770.16662530270798
4.83-5.080.2261740.16842541271597
5.08-5.40.22511780.17832508268696
5.4-5.820.24181740.18922552272697
5.82-6.40.22841790.19062542272199
6.4-7.320.25891800.19562547272798
7.33-9.220.20671770.15432557273497
9.22-47.290.21341530.16852284243788

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