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- PDB-9kow: Crystal structure of RaTG13 RBD complexed with cattle ACE2 -

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Basic information

Entry
Database: PDB / ID: 9kow
TitleCrystal structure of RaTG13 RBD complexed with cattle ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • RaTG13 RBD
KeywordsVIRAL PROTEIN/HYDROLASE / RaTG13 RBD / cattle ACE2 / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / virus receptor activity / cilium / apical plasma membrane / cell surface / proteolysis ...angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / virus receptor activity / cilium / apical plasma membrane / cell surface / proteolysis / extracellular space / metal ion binding / plasma membrane / 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. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Bat coronavirus RaTG13
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.98 Å
AuthorsLan, J. / Wang, C.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RaTG13 RBD complexed with cattle ACE2
Authors: Lan, J. / Wang, C.H.
History
DepositionNov 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
E: RaTG13 RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3284
Polymers91,5202
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.526, 97.319, 90.534
Angle α, β, γ (deg.)90.00, 129.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 69701.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ACE2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q58DD0
#2: Protein RaTG13 RBD


Mass: 21818.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Current sequence matches UniProt ID A0A6B9WHD3 with TAX ID 2709072 (Bat coronavirus RaTG13). However, UniProt ID A0A6B9WHD3 is deleted from UniProtKB and can be found in UniParc, https://www. ...Details: Current sequence matches UniProt ID A0A6B9WHD3 with TAX ID 2709072 (Bat coronavirus RaTG13). However, UniProt ID A0A6B9WHD3 is deleted from UniProtKB and can be found in UniParc, https://www.uniprot.org/uniparc/UPI001398EDBE/entry.
Source: (gene. exp.) Bat coronavirus RaTG13 / Production host: Trichoplusia ni (cabbage looper)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 1 / 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
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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Sodium citrate tribasic dihydrate pH 5.0 10% w/v Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.98→70.09 Å / Num. obs: 8219 / % possible obs: 99.67 % / Redundancy: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 9.4
Reflection shellResolution: 3.98→4.12 Å / Num. unique obs: 829 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.98→69.09 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 838 10.2 %
Rwork0.2052 --
obs0.2122 8219 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.98→69.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6430 0 53 0 6483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046664
X-RAY DIFFRACTIONf_angle_d0.7469044
X-RAY DIFFRACTIONf_dihedral_angle_d6.113896
X-RAY DIFFRACTIONf_chiral_restr0.047955
X-RAY DIFFRACTIONf_plane_restr0.0051156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.98-4.230.33641400.25061227X-RAY DIFFRACTION100
4.23-4.550.2781330.2191237X-RAY DIFFRACTION100
4.55-5.010.25031380.211217X-RAY DIFFRACTION100
5.01-5.730.2781450.2141225X-RAY DIFFRACTION100
5.73-7.220.29551490.21321220X-RAY DIFFRACTION100
7.23-69.090.23281330.16871255X-RAY DIFFRACTION99
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)
13.9535-3.1244-0.61594.0895-0.07742.25270.3726-0.61240.0045-0.2940.4925-0.7434-0.33790.8719-0.37250.91060.0615-0.031.2682-0.31741.205160.2018-20.373910.342
23.1219-2.4859-2.03032.1210.99973.4150.19190.6079-0.8158-0.64120.2165-0.26340.1085-0.6838-0.39080.9285-0.0082-0.05070.8566-0.18380.877155.4661-22.61683.273
34.08880.64480.93873.5915-0.58963.1410.04410.22131.4825-0.75720.3565-0.812-0.77290.5135-0.14120.9605-0.29780.16491.0150.10160.826730.2113-7.6823-13.0191
43.6575-1.01751.86812.579-0.12763.2558-0.06430.0332-0.2140.0730.3639-0.2736-0.31080.4832-0.3610.6628-0.0757-0.05070.51590.00810.721125.4218-21.20240.7414
55.99123.45191.49122.37170.87571.9723-0.28720.28740.94950.1439-0.0546-0.1678-0.55860.06610.45241.2497-0.04650.0290.58330.12861.034535.1143.125121.2719
62.4288-0.43760.82744.45020.05662.66340.17140.1214-0.17980.0072-0.0859-0.0878-0.52540.1754-0.12530.906-0.0143-0.1470.6742-0.07730.719839.155-4.600816.4216
73.46480.75040.93921.9080.46695.1026-0.21430.1772-0.03750.06460.20550.0316-0.09780.15350.01650.62620.0199-0.06270.4057-0.05380.746227.7267-19.22458.5389
84.7949-0.1753-0.761.96931.3242.6008-0.34970.45190.04710.2845-0.09790.24480.3632-0.74890.33820.72260.0196-0.10050.58330.01021.08699.5735-16.08547.7952
90.9624-1.85450.59014.0288-0.98630.39590.22641.34491.79860.189-0.2005-0.98630.3016-0.0768-0.23631.1315-0.49890.12512.42440.15951.433684.8508-6.65929.5617
107.67190.69947.12220.26540.04738.5641-0.717-0.31191.268-0.70180.3564-1.0862-1.58161.15320.57661.3861-0.3026-0.40642.0996-0.13441.559877.8593-5.467742.3447
110.6126-0.0103-1.4529-0.01590.03333.4244-0.3610.3105-0.0271-0.13970.4873-0.80950.17921.0663-0.30440.8987-0.1311-0.07311.8813-0.15541.304473.0817-14.925425.9679
120.3880.29120.45040.57380.23160.4956-0.2701-0.59290.14440.27621.0959-0.4421-0.14921.3967-0.63871.24130.1295-0.00231.6125-0.42781.441475.7978-27.748913.6122
130.22330.78120.32722.61440.95181.3907-0.05050.7009-0.4568-0.07240.1018-0.54720.26260.5781-0.25970.8748-0.23060.05621.90840.00881.553476.5275-9.653230.0052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 329 )
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 431 )
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 580 )
8X-RAY DIFFRACTION8chain 'A' and (resid 581 through 614 )
9X-RAY DIFFRACTION9chain 'E' and (resid 335 through 364 )
10X-RAY DIFFRACTION10chain 'E' and (resid 365 through 393 )
11X-RAY DIFFRACTION11chain 'E' and (resid 394 through 459 )
12X-RAY DIFFRACTION12chain 'E' and (resid 460 through 494 )
13X-RAY DIFFRACTION13chain 'E' and (resid 495 through 526 )

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