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- PDB-7xbg: The crystal structure of RshSTT182/200 RBD-insert2-T346R-Y496G mu... -

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Basic information

Entry
Database: PDB / ID: 7xbg
TitleThe crystal structure of RshSTT182/200 RBD-insert2-T346R-Y496G mutant in complex with human ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • RshSTT182/200 coronavirus receptor binding domain insert2 mutant
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 cardiac conduction / regulation of vasoconstriction ...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 cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 / extracellular exosome / zinc ion binding / extracellular region / 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: 3.37 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
A: Processed angiotensin-converting enzyme 2
B: RshSTT182/200 coronavirus receptor binding domain insert2 mutant
C: Processed angiotensin-converting enzyme 2
D: RshSTT182/200 coronavirus receptor binding domain insert2 mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,07417
Polymers193,1044
Non-polymers2,97013
Water00
1
A: Processed angiotensin-converting enzyme 2
B: RshSTT182/200 coronavirus receptor binding domain insert2 mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9459
Polymers96,5522
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 mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1308
Polymers96,5522
Non-polymers1,5786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.127, 121.435, 110.488
Angle α, β, γ (deg.)90.000, 92.010, 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 mutant


Mass: 27270.062 Da / Num. of mol.: 2 / Mutation: T346R, Y496G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinolophus shameli (Shamel's horseshoe bat)
Production host: Homo sapiens (human)
#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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / 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
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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M imidazole malate pH7.0, 20% w/v PEG 4000

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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: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.37→50 Å / Num. obs: 30335 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 113.44 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 10.5
Reflection shellResolution: 3.37→3.5 Å / Rmerge(I) obs: 1.444 / Mean I/σ(I) obs: 1 / Num. unique obs: 3024

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.37→46.4 Å / SU ML: 0.4957 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 1995 6.61 %
Rwork0.2692 28168 -
obs0.2695 30163 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 156.29 Å2
Refinement stepCycle: LAST / Resolution: 3.37→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12840 0 184 0 13024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002913382
X-RAY DIFFRACTIONf_angle_d0.606218187
X-RAY DIFFRACTIONf_chiral_restr0.04411943
X-RAY DIFFRACTIONf_plane_restr0.0042337
X-RAY DIFFRACTIONf_dihedral_angle_d14.52174886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.37-3.450.47081240.45131848X-RAY DIFFRACTION92.54
3.45-3.540.39011420.42072039X-RAY DIFFRACTION99.82
3.54-3.650.45421440.39472009X-RAY DIFFRACTION99.72
3.65-3.760.35981410.3662012X-RAY DIFFRACTION99.54
3.76-3.90.34431400.32392015X-RAY DIFFRACTION99.77
3.9-4.050.30151480.32422044X-RAY DIFFRACTION99.5
4.05-4.240.30071420.30912014X-RAY DIFFRACTION99.81
4.24-4.460.26631400.27891995X-RAY DIFFRACTION99.44
4.46-4.740.251440.2622039X-RAY DIFFRACTION99.68
4.74-5.110.26941490.26762008X-RAY DIFFRACTION99.54
5.11-5.620.26181450.26852039X-RAY DIFFRACTION99.77
5.62-6.430.27391440.2782044X-RAY DIFFRACTION99.95
6.43-8.090.2481450.23092059X-RAY DIFFRACTION99.95
8.1-46.40.20481470.18692003X-RAY DIFFRACTION96.28
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)
14.644847215320.421329823528-0.8964717114584.38477630595-0.07519239883094.11803300641-0.2999418618970.28904279972-0.08934735385830.5009678522560.847925389364-0.647268653415-0.3979571179010.352766585888-0.6306060169181.626399086330.1193234825220.1697034143781.7208433343-0.2968723084071.4622129276-1.3086694678132.357927330213.7557434757
22.47465646139-1.468612498010.8146785845712.44773814241.95945062545.468345047940.960633515458-0.4979155365840.7249877986030.5317662010480.57970016966-0.276299658915-1.328915955491.07572017575-1.46035947321.562388032820.1601890979340.1867290831491.06915979836-0.1703460953791.4313384795612.991006358526.03348308914.74500970107
34.413513602460.143040111582-1.09067151592.60252849572.128282081934.899841727310.0351350883524-1.03127091132-0.01756455261950.1811550316730.689920030219-0.568506805467-0.4196346984851.3734154197-0.6232495292871.479903016650.1370640906480.2653895164821.37452549616-0.2312589286291.413594499417.693960797812.8171510804-4.3101697752
42.81124297292-1.64400552052-0.1417178835214.284982555332.355053614831.67051298549-0.04702424042850.275201762386-0.370610936045-1.462750913330.02494126156010.147995476035-0.7032335254590.116401651350.007442783242071.11864870739-0.08376821763710.06058475495780.971649812125-0.04219315489580.7930069665111.8567356829222.906196719-24.5938352672
53.23008501248-0.574657537691-0.4013378347062.901055870630.529689384843.02644255512-0.218959299835-0.20033959755-0.1477828019770.4889190098960.501979027841-0.119976663495-0.05661832084430.81422609209-0.2599824952271.215489310480.04628151187290.1852021647661.19619634024-0.08723710097781.028358244215.7341173502319.7292582413-9.29307876062
64.55154981897-0.886742986503-0.3565503130982.709753784060.2421624827481.83197191249-0.233897801016-0.321630940698-0.3692540114940.6425946525350.3033379567680.6430666125970.503083230720.3489604747650.00483584688251.396283682240.1241245421270.3421074081.04585113946-0.08019869127691.35700195132-0.50500345261211.5332233097-6.08060646526
78.13849075465-0.3110332904080.7700720501264.399564030971.866326966233.14777637984-0.03358374542140.952891559009-2.039339232030.7370361747090.566263679067-0.129158574550.587742220630.446552292304-0.4051619013791.265660955950.2181417464490.2868003572471.06264932699-0.1081208490591.1776753354316.52824097911.82620772736-19.6925230606
82.68781695484-1.314428735511.092335565913.5007378086-1.892803187044.427923397390.09818317253390.53338173101-0.1876045788780.382888280654-0.1853448939721.36420450305-0.482290346355-0.1516741372680.1305383489242.18896984850.180383507840.6236454501361.50373330736-0.05237109545092.09734268262-31.798827280950.12926866369.47203314322
90.6057075256330.1013562961390.6819826692260.06070573261630.2130562056050.950106873791-0.060266162068-0.1877405993680.7648295573381.021659240350.5777249509611.19967794894-0.322556742255-0.564057810869-0.5296362066422.464413322550.2090911355930.5620814718731.89467584011-0.04271426790532.15282249422-37.859203046745.67550685472.95179083042
102.00206190584-8.97421736083-7.503033338922.018140274565.979419405465.149732925770.2411623961060.3941417552520.7053580903580.479781626488-0.3784857092621.07370906375-1.09063383483-0.6639742424130.1281776702883.271330894280.483798372253-0.01521864611583.27081900909-0.035891671212.99237891867-47.896621744641.50388899651.82532362433
112.677242742911.514931575191.108552150582.46088949605-2.009047238254.446856498160.08680900606170.243992409799-0.05923359801760.114229857168-0.01085849092170.3330660548520.0213875343455-0.9673637355750.09878082308941.806405018880.1069639974160.6883426369491.74223873503-0.2225172771122.08735221473-30.662973259335.457597844510.3038467017
120.0005515992063940.0242546012762-0.01712336122550.11025502811-0.09732322461050.09410066958090.596918514713-0.250475253243-0.2175050093720.249797494626-0.22061078019-0.203727931064-0.230087166847-0.00534485507964-0.4388610495522.31983722496-0.08339421557480.1583025387791.427561104410.1907709153271.63989246185-13.333002187646.5338801186.83992747464
134.858866489451.35748913797-1.519428074863.53046110125-0.5384251913073.86027244408-0.0558754245312-1.91425821795-0.7593332548860.273450833939-0.3207346356010.5924019666150.3223577771990.3816379292930.4112267240982.269243679260.127381681260.9484093652041.757861771690.1342958769622.21679654643-25.480760021335.607100247221.4024798907
142.793523599560.260624768161-0.5516237678572.666503001620.5335190921282.73160642654-0.058900921953-0.5511194574380.3616542283150.781302498612-0.184147760768-0.0180682805413-0.240308583738-0.9293552125340.2578042034072.350892739250.2493456326530.5101113933961.512473076590.02284998287141.42393644084-18.307359592736.03466096318.4275966576
15-0.02047388412960.0034669213780.00204571715209-0.005823583617450.00396947402441-0.002227896915550.5153196248040.367621482990.1371625661050.0962306439402-0.543013286688-0.698879432534-0.9756631028320.5141814450080.05668418542372.62772409923-0.3208215010250.5550080744342.77997632147-0.0903147142192.88110599131-52.578359684847.55190939798.18179312677
163.205054266660.371641901992-0.714162828285.44989040854-0.5508091520924.650000924510.2236957189270.0922570627974-0.8240032852330.0918214070263-0.696768727639-0.8798940591091.47034973082-0.01226702813590.4274215654371.59915399739-0.1140604963650.2412505068431.238452290510.1616731494311.5431528217917.966135144630.209133079758.5527030239
174.225976749560.633446653952-2.399474315711.88152805196-1.915467782544.05974414359-0.0139704200126-1.14020579213-1.17123449230.360754407082-0.771453180698-1.350868018991.013376510791.41847434210.829694643271.368245202840.1369335655250.1311972682531.300506578870.4393703559281.4731083873248.869711907343.319541015155.7458987536
185.276068739042.11310081744-1.193380637182.69239106225-0.4023386064223.74826307817-0.602515667580.39698539345-1.35302960572-0.221243919772-0.108810536253-0.7956409460591.17761063497-0.1843234229080.6838721633261.488126015420.005979109864880.5828754470750.8939477173230.1213000230851.5264102618337.302528532741.038709077438.786033064
194.75240051121.6136877159-2.529960888121.96699814864-0.4528630650192.92773241110.662412030913-0.2623563802090.9503484270080.372584132513-0.494971461551-0.0209806531066-0.5411383746540.141260664788-0.1719379089451.151443915410.09351871594450.1210229270221.098345426440.2052924971461.2119459532126.948166360259.445465113552.6553260073
207.091957370011.01246590416-2.538216198223.92383833881-0.2572350021034.62021922052-0.3649999753370.743132336616-0.250221681794-0.526872354416-0.164793911814-0.7565107399380.735016237949-0.3980702975780.4760722831771.03778575233-0.04217272718770.1717280224760.8991861985080.2564417615890.8988641764530.692476969748.932119969738.920283752
218.10191475942-0.269033788384-3.271858606973.41659454962-1.228930674173.837255689390.1554451340581.566440637210.604212515086-0.10696830148-0.182788735032-0.47933800218-0.239529975321-0.4959700517210.1574712247261.42030974624-0.05574617929540.4232151232621.276262559580.1936443091111.3714552960440.067026973360.007070698628.3857418225
222.473714215440.214691757412-1.668615458891.254828376130.7323762578773.454509642710.2839339247940.5515860502560.707696172435-0.1461662001690.03839883181470.767566004029-0.161098591842-1.01802307481-0.2807786326721.47124146698-0.03847058879940.09261556833281.7397177430.2226657564051.46056946396-13.312734811445.245749095478.8818117444
231.92124429367-1.16082914609-0.5101916396196.187746130220.2819453245723.045787822360.06067421238010.190529072174-0.193774241861-0.7358779345140.5241150376450.294670310195-0.0716145753322-0.401250830802-0.5411078696411.18452482381-0.353750559443-0.03603068321881.57221439620.08555515953520.964424708639-5.8079723204434.366527719568.1058193404
240.2935376124080.6543045040340.6893048490372.566768787610.8412886775831.99805874124-0.424037317269-0.249163759698-0.858822669905-0.57307661040.1638254990410.8172983157540.151526191883-0.7795112500750.2910515145131.39314503097-0.204250226919-0.03785126527771.44168402090.2312718494741.57392740527-11.118743962243.669621382273.9391094916
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 81 )AA19 - 811 - 63
22chain 'A' and (resid 82 through 157 )AA82 - 15764 - 139
33chain 'A' and (resid 158 through 275 )AA158 - 275140 - 257
44chain 'A' and (resid 276 through 317 )AA276 - 317258 - 299
55chain 'A' and (resid 318 through 493 )AA318 - 493300 - 475
66chain 'A' and (resid 494 through 581 )AA494 - 581476 - 563
77chain 'A' and (resid 582 through 614 )AA582 - 614564 - 596
88chain 'B' and (resid 333 through 353 )BH333 - 3531 - 21
99chain 'B' and (resid 354 through 380 )BH354 - 38022 - 48
1010chain 'B' and (resid 381 through 393 )BH381 - 39349 - 61
1111chain 'B' and (resid 394 through 437 )BH394 - 43762 - 105
1212chain 'B' and (resid 438 through 450 )BH438 - 450106 - 118
1313chain 'B' and (resid 451 through 469 )BH451 - 469119 - 137
1414chain 'B' and (resid 470 through 515 )BH470 - 515138 - 183
1515chain 'B' and (resid 516 through 528 )BH516 - 528184 - 196
1616chain 'C' and (resid 19 through 109 )CJ19 - 1091 - 91
1717chain 'C' and (resid 110 through 157 )CJ110 - 15792 - 139
1818chain 'C' and (resid 158 through 249 )CJ158 - 249140 - 231
1919chain 'C' and (resid 250 through 431 )CJ250 - 431232 - 413
2020chain 'C' and (resid 432 through 581 )CJ432 - 581414 - 563
2121chain 'C' and (resid 582 through 614 )CJ582 - 614564 - 596
2222chain 'D' and (resid 333 through 380 )DQ333 - 3801 - 48
2323chain 'D' and (resid 381 through 493 )DQ381 - 49349 - 161
2424chain 'D' and (resid 494 through 528 )DQ494 - 528162 - 196

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