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- PDB-7drv: Structural basis of SARS-CoV-2-closely-related bat coronavirus Ra... -

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Basic information

Entry
Database: PDB / ID: 7drv
TitleStructural basis of SARS-CoV-2-closely-related bat coronavirus RaTG13 to hACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoproteinSpike protein
KeywordsHYDROLASE/VIRAL PROTEIN / RaTG13 / RBD / SARS-CoV-2 / ACE2 / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex
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 / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction ...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 / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / endocytosis involved in viral entry into host cell / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bat coronavirus RaTG13
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsLiu, K.F. / Pan, X.Q. / Li, L.J. / Feng, Y. / Meng, Y.M. / Zhang, Y.F. / Wu, L.L. / Chen, Q. / Zheng, A.Q. / Song, C.L. ...Liu, K.F. / Pan, X.Q. / Li, L.J. / Feng, Y. / Meng, Y.M. / Zhang, Y.F. / Wu, L.L. / Chen, Q. / Zheng, A.Q. / Song, C.L. / Jia, Y.F. / Niu, S. / Qiao, C.P. / Zhao, X. / Ma, D.L. / Ma, X.P. / Tan, S.G. / Qi, J.X. / Gao, G.F. / Wang, Q.H.
CitationJournal: Cell / Year: 2021
Title: Binding and molecular basis of the bat coronavirus RaTG13 virus to ACE2 in humans and other species.
Authors: Liu, K. / Pan, X. / Li, L. / Yu, F. / Zheng, A. / Du, P. / Han, P. / Meng, Y. / Zhang, Y. / Wu, L. / Chen, Q. / Song, C. / Jia, Y. / Niu, S. / Lu, D. / Qiao, C. / Chen, Z. / Ma, D. / Ma, X. ...Authors: Liu, K. / Pan, X. / Li, L. / Yu, F. / Zheng, A. / Du, P. / Han, P. / Meng, Y. / Zhang, Y. / Wu, L. / Chen, Q. / Song, C. / Jia, Y. / Niu, S. / Lu, D. / Qiao, C. / Chen, Z. / Ma, D. / Ma, X. / Tan, S. / Zhao, X. / Qi, J. / Gao, G.F. / Wang, Q.
History
DepositionDec 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)190,88814
Polymers188,3784
Non-polymers2,51010
Water0
1
A: Angiotensin-converting enzyme 2
C: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9889
Polymers94,1892
Non-polymers1,7997
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme 2
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9005
Polymers94,1892
Non-polymers7113
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.276, 122.875, 110.742
Angle α, β, γ (deg.)90.000, 95.067, 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 2 / / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69038.578 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: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Spike glycoprotein / Spike protein


Mass: 25150.430 Da / Num. of mol.: 2 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus RaTG13
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A6B9WHD3
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / 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: 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

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M succinic acid pH 7.0, 0.1 M bicine pH 8.5, 30% v/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.09→48.94 Å / Num. obs: 39622 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 94.99 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.3
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 1.31 / Num. unique obs: 3806

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.09→48.94 Å / SU ML: 0.5023 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 1934 4.89 %
Rwork0.226 37644 -
obs0.2272 39578 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.66 Å2
Refinement stepCycle: LAST / Resolution: 3.09→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12760 0 156 0 12916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001713278
X-RAY DIFFRACTIONf_angle_d0.477818058
X-RAY DIFFRACTIONf_chiral_restr0.03861920
X-RAY DIFFRACTIONf_plane_restr0.00392336
X-RAY DIFFRACTIONf_dihedral_angle_d22.74194823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.41611190.3662581X-RAY DIFFRACTION95.58
3.17-3.250.40581360.34512684X-RAY DIFFRACTION99.09
3.25-3.350.36641520.332636X-RAY DIFFRACTION99.64
3.35-3.460.30861570.2982692X-RAY DIFFRACTION99.62
3.46-3.580.30981230.27662688X-RAY DIFFRACTION99.57
3.58-3.720.31571120.25882702X-RAY DIFFRACTION99.61
3.72-3.890.27471540.23612655X-RAY DIFFRACTION99.29
3.89-4.10.23071530.2192729X-RAY DIFFRACTION99.83
4.1-4.350.25741500.20392644X-RAY DIFFRACTION99.86
4.35-4.690.2051240.18872716X-RAY DIFFRACTION99.89
4.69-5.160.19751560.18592693X-RAY DIFFRACTION99.93
5.16-5.910.25741290.21412737X-RAY DIFFRACTION100
5.91-7.440.27471330.23532728X-RAY DIFFRACTION100
7.44-48.940.19611360.19692759X-RAY DIFFRACTION99.38
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)
11.383840778920.57703761664-1.067111118560.579045081969-0.4339054382141.18689421118-0.2000606197090.303154407939-0.133474879105-0.1561107066690.0951535733284-0.103403321240.193767866783-0.08350869386385.19732180989E-110.649671983916-0.0222437139023-0.1128209120960.652608076780.048465904730.70865232088227.8645881054-27.537881334146.90656935
20.946524643535-0.04546575467930.0261218072250.826123551346-0.8282832312750.779146814051-0.1965696353680.147130757137-0.173953594404-0.4708810806790.110687803273-0.2736931883540.303731560721-0.11680026546-0.0007407320098670.855068083758-0.03418570546950.2059040323360.610629539749-0.02242112731840.57033865164-8.553566333022.682577428464.25863508564
30.365706925656-0.0362485382552-0.3334561922170.52211200537-0.2252339878920.699462783579-0.07186516462850.0982832083448-0.07451356930930.1890833797190.1174312685580.360740554170.0108164092552-0.4421486226774.08094535497E-90.686885174962-0.0574504387677-0.09168195790950.7365971326340.005734322552430.776646106589-10.8806493088-36.617303222472.6031099794
40.1680198914810.0402699524681-0.1786605727930.1440803707870.1253300361660.395829029041-0.111124063740.3025142936710.0631937035905-0.25746334918-0.647448574161-0.672711823842-0.1026625700990.303885189258-0.09158550656721.299686258510.03780933200250.3181903555591.549441730470.6450035612781.6366702831529.110792167825.1427575712-12.1654008163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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