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- PDB-9kos: Crystal structure of RaTG13 RBD complexed with sheep ACE2 -

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Basic information

Entry
Database: PDB / ID: 9kos
TitleCrystal structure of RaTG13 RBD complexed with sheep ACE2
Components
  • Angiotensin-converting enzyme
  • RaTG13 RBD
KeywordsVIRAL PROTEIN/HYDROLASE / RaTG13 RBD / sheep ACE2 / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / apical plasma membrane / cilium / 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 speciesOvis aries (sheep)
Bat coronavirus RaTG13
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsLan, J. / Wang, C.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RaTG13 RBD complexed with sheep 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: Angiotensin-converting enzyme
E: RaTG13 RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9233
Polymers91,7022
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.965, 171.965, 85.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Angiotensin-converting enzyme


Mass: 69745.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: JEQ12_019702 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A6P3TFC0, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein RaTG13 RBD


Mass: 21956.645 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: 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 / 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
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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BICINE pH 8.5 20% w/v Polyethylene glycol 10,000

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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: 3.74→50 Å / Num. obs: 13706 / % possible obs: 99.77 % / Redundancy: 25.1 % / CC1/2: 0.994 / Net I/σ(I): 8.8
Reflection shellResolution: 3.74→3.87 Å / Num. unique obs: 1334 / CC1/2: 0.84

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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: 3.74→49.51 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 1370 10.01 %
Rwork0.2316 --
obs0.2361 13689 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.74→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 14 0 6472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046651
X-RAY DIFFRACTIONf_angle_d0.7189025
X-RAY DIFFRACTIONf_dihedral_angle_d5.42878
X-RAY DIFFRACTIONf_chiral_restr0.044944
X-RAY DIFFRACTIONf_plane_restr0.0061158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.74-3.870.3331330.30271199X-RAY DIFFRACTION100
3.87-4.030.34161350.29931200X-RAY DIFFRACTION100
4.03-4.210.32431330.27431205X-RAY DIFFRACTION100
4.21-4.430.3031340.25971214X-RAY DIFFRACTION100
4.43-4.710.31441360.22111211X-RAY DIFFRACTION100
4.71-5.080.26091360.22331226X-RAY DIFFRACTION100
5.08-5.580.23991360.23311222X-RAY DIFFRACTION100
5.59-6.390.33521390.24411251X-RAY DIFFRACTION100
6.39-8.050.20951390.22051260X-RAY DIFFRACTION100
8.05-49.510.2381490.1771331X-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)
11.2665-0.4612-0.40363.5576-0.54162.58390.5682-0.0165-0.13040.6714-0.1373-0.070.4096-0.1531-0.27691.3498-0.072-0.11741.0662-0.17751.119754.0528-4.537429.3874
20.9443-0.0253-0.0921.8476-1.18285.4941-0.06590.0328-0.1565-0.31590.2003-0.85-1.15011.86860.23960.8286-0.0714-0.11020.9658-0.0791.05966.6235-24.86733.726
31.47660.03571.37522.16790.20921.72610.0334-0.2163-0.09930.0225-0.05670.1788-0.14770.07090.0610.6183-0.14030.03530.77910.05910.884846.6739-23.77475.4722
40.75251.47530.91880.34111.78311.228-0.27170.22160.279-0.04120.22980.14390.21730.22460.00231.23850.0532-0.05880.8479-0.03821.001353.97120.2036-0.5848
51.95820.26380.62671.61612.34912.34920.0942-0.10740.0924-0.3841-0.14540.0874-0.1991-0.36110.07630.87670.0084-0.01210.7815-0.00590.815743.2246-17.85991.088
60.7598-1.5970.12393.67081.37323.4955-0.1727-0.4130.69791.69250.7244-1.08450.40640.7085-0.35250.83820.1081-0.0710.88-0.01641.02862.38333.12432.497
74.83631.55351.02894.2429-0.79640.54760.03951.40520.26730.23870.3448-0.6217-0.2910.9672-0.35011.1431-0.0180.14241.2487-0.14731.091657.207638.159221.3712
81.07540.6593-0.10061.0959-0.50390.44980.0144-0.77640.44560.6242-0.2618-0.2205-0.22060.2729-0.36881.2090.24850.08761.12050.0771.235949.807243.750424.5232
92.4161-0.2237-0.42123.2241-0.18431.01920.16010.2914-0.06040.2651-0.04190.08860.0276-0.3332-0.07630.84640.0644-0.00180.7189-0.02920.913153.35222.281331.7697
103.9124.321-0.45834.6937-0.51950.075-0.8442-1.69961.45361.20360.30051.21920.3561-0.04150.58821.9373-0.08160.18280.9941-0.22271.404849.88116.314548.8288
112.65450.2885-0.87310.7151-0.89863.5154-0.03470.34-0.32821.1605-0.237-0.5830.2996-0.31110.32171.0275-0.0041-0.10630.6499-0.12430.814356.110620.726133.2408
121.99991.99791.99971.99771.99981.9993-1.319-1.88562.66520.35740.8402-0.8979-0.0313-0.11450.50.3523-0.3913-1.17151.43520.60681.371558.013852.019122.1111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 430 )
5X-RAY DIFFRACTION5chain 'A' and (resid 431 through 644 )
6X-RAY DIFFRACTION6chain 'E' and (resid 333 through 358 )
7X-RAY DIFFRACTION7chain 'E' and (resid 359 through 379 )
8X-RAY DIFFRACTION8chain 'E' and (resid 380 through 393 )
9X-RAY DIFFRACTION9chain 'E' and (resid 394 through 469 )
10X-RAY DIFFRACTION10chain 'E' and (resid 470 through 479 )
11X-RAY DIFFRACTION11chain 'E' and (resid 480 through 526 )
12X-RAY DIFFRACTION12chain 'E' and (resid 527 through 527 )

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