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- PDB-7w6r: Structure of Bat coronavirus RaTG13 spike receptor-binding domain... -

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Basic information

Entry
Database: PDB / ID: 7w6r
TitleStructure of Bat coronavirus RaTG13 spike receptor-binding domain complexed with its receptor equine ACE2
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular region / metal ion binding / 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. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
Similarity search - Component
Biological speciesEquus caballus (horse)
Bat coronavirus RaTG13
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXu, Z.P. / Liu, K.F. / Han, P. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100752 China
CitationJournal: Nat Commun / Year: 2022
Title: Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses
Authors: Xu, Z. / Kang, X. / Han, P. / Du, P. / Li, L. / Zheng, A. / Deng, C. / Qi, J. / Zhao, X. / Wang, Q. / Liu, K. / Gao, G.F.
History
DepositionDec 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,2144
Polymers94,9282
Non-polymers2872
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, crystal sructure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-40 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.782, 122.837, 68.797
Angle α, β, γ (deg.)90.000, 92.420, 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

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Components

#1: Protein Angiotensin-converting enzyme


Mass: 69777.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: ACE2 / Production host: Escherichia coli (E. coli)
References: UniProt: F6V9L3, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike glycoprotein


Mass: 25150.430 Da / Num. of mol.: 1 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus RaTG13 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A6B9WHD3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#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 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium chloride, 0.1M Tris 8.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 32977 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 42.55 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.075 / Rrim(I) all: 0.187 / Rsym value: 0.171 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3285 / CC1/2: 0.793 / Rpim(I) all: 0.448 / Rsym value: 1.032 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.6→46.16 Å / SU ML: 0.2429 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 2014 6.56 %
Rwork0.1923 28700 -
obs0.1924 30714 92.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 15 166 6591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356605
X-RAY DIFFRACTIONf_angle_d0.69538973
X-RAY DIFFRACTIONf_chiral_restr0.0464941
X-RAY DIFFRACTIONf_plane_restr0.00621158
X-RAY DIFFRACTIONf_dihedral_angle_d16.52382405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.2771050.27461384X-RAY DIFFRACTION62.48
2.67-2.740.25481150.25791565X-RAY DIFFRACTION72.04
2.74-2.820.23591180.24051793X-RAY DIFFRACTION81.01
2.82-2.910.26221470.25421952X-RAY DIFFRACTION89.93
2.91-3.010.28131460.26542165X-RAY DIFFRACTION97.47
3.01-3.130.25031460.24972173X-RAY DIFFRACTION98.56
3.13-3.280.23411580.24072192X-RAY DIFFRACTION99.66
3.28-3.450.21811600.2252185X-RAY DIFFRACTION99.66
3.45-3.670.21531420.21042194X-RAY DIFFRACTION99.83
3.67-3.950.17291540.18322207X-RAY DIFFRACTION99.83
3.95-4.350.15561480.15612220X-RAY DIFFRACTION99.92
4.35-4.970.14161610.14132220X-RAY DIFFRACTION99.92
4.97-6.260.17981570.16232199X-RAY DIFFRACTION99.96
6.26-46.160.15371570.15362251X-RAY DIFFRACTION99.67
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)
10.7199504532780.324060076139-0.0950738217691-0.108721239366-0.105336420075-0.214238566705-0.09777472353190.021602058076-0.0292592777768-0.1882618800320.0989732251286-0.0121828292933-0.0188428937937-0.01026025149860.01037252491520.419575623539-0.00252102023733-0.003254337888910.383873219328-0.03300463989820.372611191036-6.919378377169.9239302908-8.04226332682
20.6914645719920.409532564513-0.220940509270.7608999838-0.03433782224080.9660300588970.0176319706004-0.0276040924610.04385204821060.0276237352309-0.02628677550620.00233914081568-0.07227867088940.07807282559330.005361194497820.23955976923-0.00392764848293-0.01069088277690.1997145561720.004303197659190.23721816304413.192170748388.8363760085.29386939821
30.7195854130940.2476587761880.2642653603281.005264303590.2786219476111.177011197980.17920224769-0.0138658028503-0.09597279438020.107321092874-0.0545309545112-0.1288923065450.2103066098-0.0480838084474-0.06282397070090.308431937306-0.02168659885510.008951732968120.3224421916180.005195537506450.299550984344-3.1490545703872.355498918216.5328929519
40.4462504546280.28820383006-0.1196729755650.679843273089-0.2048435330180.8651405028310.0383294692412-0.05729843939840.132009636370.0567631212445-0.07364020515790.103788947961-0.195743112296-0.04237188380610.03744437548670.281759604568-0.0108839150255-0.003894050668130.259878338702-0.01529483593760.3037679051624.0829233394794.03470404957.68185705688
50.9605050873640.0453728204058-0.3761973479360.282511628312-0.1985513984570.386473364075-0.0290108134574-0.33219912985-0.1809362400960.1591387257080.0567669809770.1369609735570.0882001592087-0.036911614185-0.01400647711960.396633682254-0.01656792566940.02181921130650.4058667121510.02962423337810.388447690528-39.740760009951.198002379518.4398880402
60.900422972964-0.1821129778250.09497509059051.29584929376-0.3667070319091.374784410050.07006761679920.001071200488650.0377376818781-0.0827786513805-0.01561776993710.1019398003520.0213648272268-0.0563848427984-0.0508463765210.2221130827070.00714120953564-0.01610821757490.237133590086-0.01974277113350.304241632912-29.725336990159.43834761341.69957510268
71.885535766710.1716757505340.1595599799110.6778708307620.07288555321130.5058170806710.0936980799773-0.556200736297-0.3590761675840.133475699817-0.02282859258860.3660559642580.177707064046-0.0465583600650.003342542666880.341675334773-0.02298054720350.04203093867990.3612967917880.02267603135050.474553960786-45.490703312350.777070670917.1054962632
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 128 )AA19 - 1281 - 110
22chain 'A' and (resid 129 through 317 )AA129 - 317111 - 299
33chain 'A' and (resid 318 through 387 )AA318 - 387300 - 369
44chain 'A' and (resid 388 through 614 )AA388 - 614370 - 596
55chain 'B' and (resid 334 through 393 )BB334 - 3931 - 60
66chain 'B' and (resid 394 through 506 )BB394 - 50661 - 173
77chain 'B' and (resid 507 through 529 )BB507 - 529174 - 196

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