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- PDB-7xbh: The complex structure of RshSTT182/200 RBD bound to human ACE2 -

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Basic information

Entry
Database: PDB / ID: 7xbh
TitleThe complex structure of RshSTT182/200 RBD bound to human ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • RshSTT182/200 coronavirus receptor binding domain
KeywordsVIRAL 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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / 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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / 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 / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / 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 / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / 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.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesRhinolophus shameli (Shamel's horseshoe bat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsHu, Y. / Liu, K.F. / Han, P. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Embo J. / Year: 2023
Title: Host range and structural analysis of bat-origin RshSTT182/200 coronavirus binding to human ACE2 and its animal orthologs.
Authors: Hu, Y. / Liu, K. / Han, P. / Xu, Z. / Zheng, A. / Pan, X. / Jia, Y. / Su, C. / Tang, L. / Wu, L. / Bai, B. / Zhao, X. / Tian, D. / Chen, Z. / Qi, J. / Wang, Q. / Gao, G.F.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.name
Revision 1.2Nov 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
B: RshSTT182/200 coronavirus receptor binding domain
A: Processed angiotensin-converting enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4888
Polymers94,3162
Non-polymers1,1716
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.413, 155.229, 60.996
Angle α, β, γ (deg.)90.000, 103.661, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein RshSTT182/200 coronavirus receptor binding domain


Mass: 24576.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinolophus shameli (Shamel's horseshoe bat)
Production host: Homo sapiens (human)
#2: Protein Processed angiotensin-converting enzyme 2


Mass: 69739.344 Da / Num. of mol.: 1
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
#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.: 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
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.01M sodium borate pH 8.5, 1.0M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.72→33.42 Å / Num. obs: 37596 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 75.07 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.4
Reflection shellResolution: 2.72→2.92 Å / Rmerge(I) obs: 2.842 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2783

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.02→29.64 Å / SU ML: 0.4078 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1421 5.17 %
Rwork0.2006 26087 -
obs0.2023 27508 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.66 Å2
Refinement stepCycle: LAST / Resolution: 3.02→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 71 5 6607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326784
X-RAY DIFFRACTIONf_angle_d0.58939223
X-RAY DIFFRACTIONf_chiral_restr0.0489986
X-RAY DIFFRACTIONf_plane_restr0.00491186
X-RAY DIFFRACTIONf_dihedral_angle_d15.1722460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.120.39171460.32962629X-RAY DIFFRACTION99.93
3.12-3.250.33981470.2882616X-RAY DIFFRACTION99.89
3.25-3.40.28741410.2562616X-RAY DIFFRACTION99.82
3.4-3.580.26181430.23372592X-RAY DIFFRACTION99.89
3.58-3.80.25271390.21042628X-RAY DIFFRACTION99.96
3.8-4.090.23021420.18592601X-RAY DIFFRACTION99.53
4.09-4.50.20521340.17252613X-RAY DIFFRACTION99.85
4.5-5.150.18741490.16482611X-RAY DIFFRACTION99.78
5.15-6.480.23641350.19912639X-RAY DIFFRACTION99.57
6.48-29.640.20321450.17662542X-RAY DIFFRACTION95.55

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