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- PDB-7c8j: Structural basis for cross-species recognition of COVID-19 virus ... -

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Basic information

Entry
Database: PDB / ID: 7c8j
TitleStructural basis for cross-species recognition of COVID-19 virus spike receptor binding domain to bat ACE2
Components
  • Angiotensin-converting enzyme
  • SARS-CoV-2 Receptor binding domain
KeywordsVIRAL PROTEIN/PROTEIN BINDING / COVID-19 / receptor binding domain (RBD) / Rhinolophus macrotis / bats / ACE2 / VIRAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / 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 / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / proteolysis / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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 ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesRhinolophus macrotis (Big-eared Horseshoe Bat)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsLiu, K.F. / Wang, J. / Tan, S.G. / Niu, S. / Wu, L.L. / Zhang, Y.F. / Pan, X.Q. / Meng, Y.M. / Chen, Q. / Wang, Q.H. ...Liu, K.F. / Wang, J. / Tan, S.G. / Niu, S. / Wu, L.L. / Zhang, Y.F. / Pan, X.Q. / Meng, Y.M. / Chen, Q. / Wang, Q.H. / Wang, H.W. / Qi, J.X. / Gao, G.F.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cross-species recognition of SARS-CoV-2 to bat ACE2.
Authors: Kefang Liu / Shuguang Tan / Sheng Niu / Jia Wang / Lili Wu / Huan Sun / Yanfang Zhang / Xiaoqian Pan / Xiao Qu / Pei Du / Yumin Meng / Yunfei Jia / Qian Chen / Chuxia Deng / Jinghua Yan / ...Authors: Kefang Liu / Shuguang Tan / Sheng Niu / Jia Wang / Lili Wu / Huan Sun / Yanfang Zhang / Xiaoqian Pan / Xiao Qu / Pei Du / Yumin Meng / Yunfei Jia / Qian Chen / Chuxia Deng / Jinghua Yan / Hong-Wei Wang / Qihui Wang / Jianxun Qi / George Fu Gao /
Abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2- ...The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2-related coronaviruses have been isolated from bats and SARS-CoV-2 may infect bat, the structural basis for SARS-CoV-2 to utilize the human receptor counterpart bat angiotensin-converting enzyme 2 (bACE2) for virus infection remains less understood. Here, we report that the SARS-CoV-2 spike protein receptor binding domain (RBD) could bind to bACE2 from (bACE2-Rm) with substantially lower affinity compared with that to the human ACE2 (hACE2), and its infectivity to host cells expressing bACE2-Rm was confirmed with pseudotyped SARS-CoV-2 virus and SARS-CoV-2 wild virus. The structure of the SARS-CoV-2 RBD with the bACE2-Rm complex was determined, revealing a binding mode similar to that of hACE2. The analysis of binding details between SARS-CoV-2 RBD and bACE2-Rm revealed that the interacting network involving Y41 and E42 of bACE2-Rm showed substantial differences with that to hACE2. Bats have extensive species diversity and the residues for RBD binding in bACE2 receptor varied substantially among different bat species. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. These findings would benefit our understanding of the potential infection of SARS-CoV-2 in varied species of bats.
History
DepositionJun 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: SARS-CoV-2 Receptor binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2903
Polymers104,2242
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-38 kcal/mol
Surface area39530 Å2
Unit cell
Length a, b, c (Å)163.197, 163.197, 211.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Angiotensin-converting enzyme /


Mass: 82350.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinolophus macrotis (Big-eared Horseshoe Bat)
Gene: ACE2 / Production host: Escherichia coli (E. coli)
References: UniProt: E2DHI3, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein SARS-CoV-2 Receptor binding domain / S glycoprotein / E2 / Peplomer protein


Mass: 21873.496 Da / Num. of mol.: 1 / Fragment: UNP residues 333-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P0DTC2
#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
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: 3.38 Å3/Da / Density % sol: 63.62 %
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: SDMS / Detector: CMOS / 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: 3.18→48.1 Å / Num. obs: 22038 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 65.43 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 15.6
Reflection shellResolution: 3.18→48.1 Å / Rmerge(I) obs: 1.79

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Processing

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

6lzg


Resolution: 3.18→48.1 Å / SU ML: 0.3609 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 1108 5.03 %
Rwork0.2185 20921 -
obs0.2211 22029 90.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.21 Å2
Refinement stepCycle: LAST / Resolution: 3.18→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7317 0 0 0 7317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247520
X-RAY DIFFRACTIONf_angle_d0.682310203
X-RAY DIFFRACTIONf_chiral_restr0.04461061
X-RAY DIFFRACTIONf_plane_restr0.00511319
X-RAY DIFFRACTIONf_dihedral_angle_d23.67122770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.330.381690.30681355X-RAY DIFFRACTION47.58
3.33-3.50.299990.27842291X-RAY DIFFRACTION80.53
3.5-3.720.31261390.25382799X-RAY DIFFRACTION97.61
3.72-4.010.31691480.23612842X-RAY DIFFRACTION99.9
4.01-4.410.27951520.20642849X-RAY DIFFRACTION99.97
4.41-5.050.22711850.18812853X-RAY DIFFRACTION99.97
5.05-6.360.26851630.21072896X-RAY DIFFRACTION99.9
6.36-6.890.23561530.1973036X-RAY DIFFRACTION99.25
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)
10.4327725422060.102945036836-0.2446457831960.4882848735330.04291596411810.2547493953240.00681526116116-0.01358837460570.002068604823220.069226386488-0.002587668088480.018259066279-0.04484374652890.0954610444223-1.25006570294E-120.2734426886260.00582449916805-0.09054063505750.2023287267360.01246755552760.203914066315-58.980466985729.1308380451-25.8603968207
20.101852663182-0.0480970432590.108978385220.0900240793583-0.02984895405890.0755682195956-0.1996861866510.00249504192340.1310361190830.1401765542550.1863431109150.09270339775430.0601135092643-0.04726297076191.45418586986E-90.4126397857340.152387909256-0.002224551661790.292473647353-0.01734885533520.384408648941-111.81679356622.8012531801-16.9498850665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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