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- PDB-7wa3: Structure of American mink ACE2 -

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Basic information

Entry
Database: PDB / ID: 7wa3
TitleStructure of American mink ACE2
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / SARS-CoV-2 spike receptor-binding domain
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / cilium / apical plasma membrane / proteolysis / extracellular space / metal ion binding / cytoplasm
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.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesNeovison vison (American mink)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsSu, C. / Qi, J.X. / Gao, G.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The molecular basis of SARS-CoV-2 variants binding to mink ACE2
Authors: Su, C. / He, J.H. / Qi, J.X. / Yang, M.S. / Wang, Q.H. / Gao, G.F.
History
DepositionDec 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 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 1.2Nov 13, 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: Angiotensin-converting enzyme
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7119
Polymers141,1242
Non-polymers1,5867
Water5,873326
1
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2915
Polymers70,5621
Non-polymers7294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-26 kcal/mol
Surface area26130 Å2
MethodPISA
2
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4194
Polymers70,5621
Non-polymers8573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-24 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.697, 97.725, 105.063
Angle α, β, γ (deg.)90.000, 91.988, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 19 through 701)
d_2ens_1(chain "B" and resid 19 through 701)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERHISA1 - 600
d_12ens_1NAGNAGB
d_13ens_1NAGNAGC
d_21ens_1SERHISF1 - 600
d_22ens_1NAGNAGG
d_23ens_1NAGNAGH

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Components

#1: Protein Angiotensin-converting enzyme


Mass: 70562.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neovison vison (American mink) / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A7T0Q2W2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#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.: 4 / 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Potassium thiocyanate, 30% w/v PEG 2000 MME2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.28→71.54 Å / Num. obs: 61639 / % possible obs: 98.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 32.7 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.6
Reflection shellResolution: 2.28→2.4 Å / Rmerge(I) obs: 0.591 / Num. unique obs: 9035 / CC1/2: 0.737

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R42

1r42


Resolution: 2.28→42.19 Å / SU ML: 0.3011 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 2800 4.59 %
Rwork0.2275 58259 -
obs0.2283 61059 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 2.28→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9884 0 96 326 10306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002610270
X-RAY DIFFRACTIONf_angle_d0.568213948
X-RAY DIFFRACTIONf_chiral_restr0.04091447
X-RAY DIFFRACTIONf_plane_restr0.00451802
X-RAY DIFFRACTIONf_dihedral_angle_d13.04053773
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.96243616926 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.320.33091430.3132826X-RAY DIFFRACTION95.99
2.32-2.360.31681340.30332960X-RAY DIFFRACTION99.36
2.36-2.40.34241780.28912944X-RAY DIFFRACTION99.71
2.4-2.450.2931370.29272960X-RAY DIFFRACTION99.55
2.45-2.510.29591640.27862995X-RAY DIFFRACTION99.72
2.51-2.560.33851220.27652969X-RAY DIFFRACTION99.81
2.56-2.630.27871470.26542976X-RAY DIFFRACTION99.9
2.63-2.70.2987880.2692016X-RAY DIFFRACTION66.96
2.7-2.780.26561520.25022920X-RAY DIFFRACTION99.68
2.78-2.870.26781660.26052974X-RAY DIFFRACTION99.81
2.87-2.970.27871410.25962992X-RAY DIFFRACTION99.68
2.97-3.090.2741790.25632949X-RAY DIFFRACTION99.59
3.09-3.230.28041310.2532955X-RAY DIFFRACTION99.1
3.23-3.40.29191410.23682978X-RAY DIFFRACTION98.86
3.4-3.610.23251600.2222910X-RAY DIFFRACTION98.18
3.61-3.890.24221200.20812967X-RAY DIFFRACTION98.44
3.89-4.280.18951340.18782956X-RAY DIFFRACTION98.66
4.28-4.90.16791030.1793014X-RAY DIFFRACTION98.27
4.9-6.170.18211240.19642975X-RAY DIFFRACTION97.85
6.17-42.190.19121360.18223023X-RAY DIFFRACTION97.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9760259584580.1747114419720.009733631215380.7258899405820.2196269671530.750990851936-0.0102652954915-0.02947954245240.0247443051050.004050242467740.0230766384696-0.008962879535460.000178519913759-0.0743226133702-0.01540081512810.208222991630.0248843458040.01545429115330.1949669070850.01464834447080.22432947877-17.281519561510.4734957779-5.45291662731
20.9063150943960.137252417309-0.01798311281810.980529005114-0.1835280805630.6462807981190.01856425803030.00506674085935-0.046906262917-0.0515739464652-0.008735138934480.02983605923280.05242602294610.0528932255009-0.01384890834320.227147707870.0355743935659-0.01236375294470.223897862341-0.02938872527750.266609631478-18.355093869515.440463482247.2134789875
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 19 - 800 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11chain AAA - E
22chain BBF - K

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