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- PDB-7xbf: The complex structure of RshSTT182/200 RBD-insert2 bound to human ACE2 -

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Basic information

Entry
Database: PDB / ID: 7xbf
TitleThe complex structure of RshSTT182/200 RBD-insert2 bound to human ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • RshSTT182/200 coronavirus receptor binding domain insert2
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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / viral translation / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
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. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rhinolophus shameli (Shamel's horseshoe bat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 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
Revision 1.3Nov 20, 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: Processed angiotensin-converting enzyme 2
B: RshSTT182/200 coronavirus receptor binding domain insert2
C: Processed angiotensin-converting enzyme 2
D: RshSTT182/200 coronavirus receptor binding domain insert2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,76817
Polymers193,2044
Non-polymers2,56413
Water00
1
A: Processed angiotensin-converting enzyme 2
B: RshSTT182/200 coronavirus receptor binding domain insert2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9959
Polymers96,6022
Non-polymers1,3937
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Processed angiotensin-converting enzyme 2
D: RshSTT182/200 coronavirus receptor binding domain insert2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7738
Polymers96,6022
Non-polymers1,1716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.391, 123.891, 112.787
Angle α, β, γ (deg.)90.000, 93.261, 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 Processed angiotensin-converting enzyme 2


Mass: 69281.805 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
#2: Protein RshSTT182/200 coronavirus receptor binding domain insert2


Mass: 27320.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinolophus shameli (Shamel's horseshoe bat)
Production host: Homo sapiens (human)
#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.: 11 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH6.0, 0.2M magnesium chloride, 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: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.51→50 Å / Num. obs: 28025 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 110.12 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9
Reflection shellResolution: 3.51→3.65 Å / Redundancy: 5 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2812 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.51→40.63 Å / SU ML: 0.4319 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2327 1438 5.14 %
Rwork0.1993 26534 -
obs0.201 27972 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.15 Å2
Refinement stepCycle: LAST / Resolution: 3.51→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13058 0 156 0 13214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002413580
X-RAY DIFFRACTIONf_angle_d0.497918465
X-RAY DIFFRACTIONf_chiral_restr0.03991975
X-RAY DIFFRACTIONf_plane_restr0.00392373
X-RAY DIFFRACTIONf_dihedral_angle_d13.65994922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.630.33451310.30622529X-RAY DIFFRACTION94.59
3.63-3.780.29981490.27222642X-RAY DIFFRACTION99.86
3.78-3.950.27991410.23952633X-RAY DIFFRACTION99.93
3.95-4.160.25411540.22532657X-RAY DIFFRACTION99.93
4.16-4.420.23581260.19622684X-RAY DIFFRACTION100
4.42-4.760.21091350.17232684X-RAY DIFFRACTION99.96
4.76-5.230.21251500.17312663X-RAY DIFFRACTION100
5.23-5.990.23631290.18732682X-RAY DIFFRACTION100
5.99-7.540.2221700.20372668X-RAY DIFFRACTION100
7.54-40.630.20511530.17542692X-RAY DIFFRACTION98.72
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)
11.45101775969-0.321452977472-0.8524122315921.151730950080.8791066644281.22638564655-0.279563183275-0.300003973214-0.1916478545720.3433169660050.3246149931610.09579003006460.2688470754280.325818942101-3.22155225887E-70.6964988281570.107804702998-0.03429118581370.7432019948760.003591805189390.5842513504697.7499716074118.6625097752-4.80998777138
20.471847196604-0.159635922234-0.2051380076150.402332870803-0.04177936826160.655398500622-0.206352093797-0.2355657738590.08376640139810.4141453629630.0202791215660.515770090089-0.0820249928115-0.1166461841517.06882813473E-91.313460756510.009695519082660.2969911851821.21357230627-0.1606905303391.53395230844-31.761567793542.08457560810.823431656
32.846219998141.84945771423-2.105618251241.45007993035-1.516778005322.35154186017-0.128409396730.127999125178-0.182715066604-0.112314888474-0.0684827653685-0.2704439724040.30648985791-0.00440003013178-0.002776231700630.6518931079760.0548446619895-0.06038302593440.5573518424310.1067864609470.7130186955829.547033583749.001289707847.6123470899
40.2778038413880.208085538844-0.4203472863311.1157134551-0.498244558080.524935753671-0.04702765298290.2241562260130.331051316397-0.08277374317920.1987105431440.179014312905-0.0754469392954-0.4924723395218.25386606552E-90.817460715858-0.0166042491989-0.09626583716481.009576016330.07331233006050.900876685651-11.092728785840.123582581274.9090641305
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain AAA - G19 - 2001
22chain BBH - I314 - 688
33chain CCJ - O19 - 2001
44chain DDP - Q314 - 523

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