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- PDB-8ysf: MERS-CoV RBD in complex with nanobody Nb9 -

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Basic information

Entry
Database: PDB / ID: 8ysf
TitleMERS-CoV RBD in complex with nanobody Nb9
Components
  • Nb9
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / MERS-CoV nanobody Nb9
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsWang, Y.X. / Ma, S.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908500 China
National Natural Science Foundation of China (NSFC)31971127 China
National Natural Science Foundation of China (NSFC)81801998 China
CitationJournal: Plos Pathog. / Year: 2024
Title: Structure defining of ultrapotent neutralizing nanobodies against MERS-CoV with novel epitopes on receptor binding domain.
Authors: Ma, S. / Zhang, D. / Wang, Q. / Zhu, L. / Wu, X. / Ye, S. / Wang, Y.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spike glycoprotein
C: Nb9
A: Spike glycoprotein
D: Nb9


Theoretical massNumber of molelcules
Total (without water)73,0004
Polymers73,0004
Non-polymers00
Water00
1
B: Spike glycoprotein
C: Nb9


Theoretical massNumber of molelcules
Total (without water)36,5002
Polymers36,5002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-3 kcal/mol
Surface area15200 Å2
MethodPISA
2
A: Spike glycoprotein
D: Nb9


Theoretical massNumber of molelcules
Total (without water)36,5002
Polymers36,5002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-3 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.819, 85.819, 248.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 23473.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Virus-associated RNAs (TAX ID 1425366) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID R9UQ53 with TAX ID 1335626 ...Details: Sequence reference for Virus-associated RNAs (TAX ID 1425366) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID R9UQ53 with TAX ID 1335626 (Middle East respiratory syndrome-related coronavirus) which matches the entry title.
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Insecta environmental sample (insect) / References: UniProt: R9UQ53
#2: Antibody Nb9


Mass: 13026.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia (bacteria)
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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 24% PEG1500,100mM SPG, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 24412 / % possible obs: 98.27 % / Redundancy: 20 % / Biso Wilson estimate: 88.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.6
Reflection shellResolution: 2.76→2.8 Å / Num. unique obs: 2333 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→37.34 Å / SU ML: 0.3981 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.27 1254 5.14 %
Rwork0.2327 23131 -
obs0.2347 24385 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.98 Å2
Refinement stepCycle: LAST / Resolution: 2.76→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 0 0 5014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325125
X-RAY DIFFRACTIONf_angle_d0.69826976
X-RAY DIFFRACTIONf_chiral_restr0.0418791
X-RAY DIFFRACTIONf_plane_restr0.0042893
X-RAY DIFFRACTIONf_dihedral_angle_d10.52251850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.870.34921270.29262443X-RAY DIFFRACTION96.04
2.87-30.36161080.29092522X-RAY DIFFRACTION97.81
3-3.160.37271460.32162501X-RAY DIFFRACTION97.96
3.16-3.360.33641440.28492532X-RAY DIFFRACTION98.85
3.36-3.620.28631380.25622574X-RAY DIFFRACTION99.12
3.62-3.980.28271640.23712542X-RAY DIFFRACTION99.3
3.98-4.560.27061490.21582591X-RAY DIFFRACTION98.7
4.56-5.740.22671330.20882634X-RAY DIFFRACTION98.57
5.74-37.340.24751450.21862792X-RAY DIFFRACTION98.62
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)
13.32048682376-0.7847538841311.271362704966.58863368477-4.673623328634.75176838531-0.131903779713-0.07502358107290.4222062654190.3003019862090.08285147969650.2203578647870.10362484183-0.4966561485370.1162742655320.907918040284-0.027047755186-0.1295659091890.602604213657-0.07135345935810.7115650509154.3769374917418.915484715617.6017875038
26.24108760172.192196255343.170663345455.218079602890.3737110473663.44045106922-0.04343949916070.00614287104691-0.0373708884155-0.367693017578-0.1547450096970.0738890580980.167447951363-0.4051353738740.1399293273341.094386328070.04592343569650.06471123308690.5437585535340.003823048444240.70362054703116.49896137119.6796924278528.2502640452
32.520148557790.8139936769371.458268243653.35339041022-1.123757821023.814836457420.339680795579-0.0852664236903-0.181612775612-0.501421121744-0.2584181077550.2398206476170.552328965675-0.325583046439-0.1161837121460.891462426220.03746645522890.09070062048090.51015442563-0.1495735193230.61333633491112.433003411217.162949478220.7199935698
47.562444970753.269679575564.79709680694.22486965571-0.09524644262135.04568287633-0.396494031618-0.7140329898540.5528503274930.858894083571-0.062740920166-0.2297609198350.321119665183-0.306987324750.5850967465541.40240820673-0.03292662419980.07608280773750.816136970185-0.1599662244440.87749952757127.924035972834.361571655945.1952171665
54.210838366734.129550128970.3779176332784.489513277391.322932873012.429047650830.9353510283271.41325652547-0.5529110899790.541124811753-1.613157135340.858639146919-0.668537064488-0.735569349430.6521979708790.9887930267690.102003483501-0.1736147139520.918749819744-0.08141159028961.464407089639.7572396883732.295682068661.4963037792
62.002556238255.15880607998-1.405713337193.0630310416-2.660342435097.554299983690.773752665307-0.961899130921.73808895877-0.491236154761-0.5529228616461.76269989497-1.65200066193-1.39026848335-0.3344461402951.70513888241-0.2467233884680.1946195233780.819145626178-0.2761278032381.2191069216117.569673175335.26313336648.2647905001
76.053652662754.316185080252.602087548397.240157145441.740137965872.86658523753-0.02707894197721.220581806081.9444929423-0.4637728571870.7628750341710.396294568561-1.348665135511.78099530811-0.4517077185411.873107819150.02161727303580.1912321694960.8570318728120.02812938880280.92630202461723.455159912632.664194341234.202143219
89.784762108644.61830837796-1.078367584535.945647704911.690951236447.658826899431.25419804269-0.5237351887610.06019489377470.289827600218-0.969555720420.354682014231-1.173804547760.146689496396-0.7020032192591.28888912369-0.104272049889-0.1821479924410.4944153871960.008463395192891.0322658721219.610393578224.699519646.8796827565
94.71472365067-2.178413349980.7898681338962.630827472093.130226194857.60757967757-0.110158195562-0.0811180243359-0.488852362644-0.04932008726160.3100671409280.664617841978-0.295192307265-0.6527571981630.08565024755781.10476246072-0.219799755469-0.09530023711260.657113613969-0.03977839856420.88155690706813.568949187623.967758248645.1222366279
103.18102141343-1.369469811611.139398708551.91621681065-0.03215506198114.5051451752-0.826632899058-0.3122670926471.04315324649-1.19323461632-0.730618249192-0.0574277079234-1.11479929167-0.2194835886990.1382453429171.62323664672-0.231862632407-0.2349416782580.4456021422820.05933139806550.90826704827715.205755997136.332655224243.9549499852
115.49937958102-1.7946738552-5.325197252663.726159229043.334997615027.235129920330.691774540779-0.657103951966-0.484953076322-0.173896032443-0.4593617566020.20989405581-0.534038252590.4430789180380.09075904771361.22227770379-0.163458101046-0.06096399826540.885387529571-0.02722010698310.70774828265816.687916565925.667891714952.0101174951
127.96341668574-2.00292267365-1.894147780635.103646230713.755313101141.9991853819-0.1126262342071.412001056090.5649037105630.158211903582-0.884383442954-1.51782966983-1.54222742757-0.120161472261-0.4164029421931.427113688270.28321228056-0.149234772410.667522200228-0.1097642407741.0543256113529.151210559124.273298239739.0324702636
135.05926185971-3.11025975406-4.547074121238.76823454047.759883751798.12046271532-1.61154936473-0.207407920287-1.602979330850.4618267011571.067612950260.8104601143063.618652606420.2999788059180.5858891797031.3963606334-0.29923565031-0.1050892859070.8884856544280.1397691258230.75342926600517.019725757630.310386798862.3019398081
145.28376337548-1.83492524035-2.168953485483.586655606650.4372385127951.81218107620.2072193840631.167246016280.268206095186-0.962707876241-0.1564870921781.1311443649-0.594148886582-0.930190134826-0.1844411809151.144729660420.283203485702-0.3196491693090.9766445717860.1061037311821.18099194944-4.3079030749152.3846829393-6.47611026035
156.410501588760.2566391354670.970054555390.792582455634-0.04586457185671.65597856514-0.2848571176450.1561650001150.478354696608-0.2369088846940.08831545879880.348951676101-0.441274989573-0.3589707486280.184302596371.070744741270.224382105475-0.1258674964610.7933899448150.08006112418680.8536399866967.6964665397145.2604425824-4.09811845837
165.454493291085.217361114654.329289246026.022801986554.188571359983.54260881986-0.3358077237832.25018282373-1.20777238917-2.914130156620.81467100401-1.68763341881-0.6990626802281.38666197757-0.006947258563361.678271144790.08231407791550.06353663290191.263524017180.2046804062810.9243314728122.968137355348.4409836784-14.3947649435
174.331881214021.65747836879-0.1502759520862.46991818873-1.308141253483.868539167150.4323817176021.143336777160.782139786342-0.360422179108-0.07743318313320.101936072693-0.312513165997-0.188208081699-0.3924522808680.8265228389150.236622086284-0.0864314242080.6435888334690.08374473972330.8068040061639.5458868709948.8398106504-5.15776978939
188.401082758212.678338874853.224569372094.20169463557-1.490213209023.23250417494-0.03163489959060.786507702908-0.715302653463-1.230403536770.686817596006-2.039367199351.185295108250.0811433218895-0.6683498847820.8348051819960.05765618210690.05714638549920.943182175483-0.2228172447080.70029050454329.337796600143.70061763820.0968847062
191.42303073-1.37001220604-1.029924402972.59083646771.801355366511.28423066843-0.986479019583-0.238359552314-0.460540946262-0.7904274868481.593812267130.5867220068130.8171420942480.22879303144-0.6312827460381.203504985470.0702328065257-0.0360491837170.9573942852630.05102092455290.82761062748724.58534016927.46671362820.0217868242
201.87573742231-0.697918212825-0.3369209078831.317260166930.3486582173336.331324659340.6586336740140.3518898538830.208642481866-0.798996753097-0.179242907895-0.215496800613-0.642125352151-0.370887466591-0.2265394399761.030271724880.0705355187290.0790911457820.6654302921820.0522817055340.78033854848120.112767999549.312568745714.913291147
219.49709838827-7.92318566587-4.794355608529.194955607983.86894588257.111094120480.89669858717-0.2689603479440.781734919846-1.147462661940.0725450132136-1.219992215440.2632931272020.722125539714-0.9249675675991.131622247330.0875295527061-0.04937892540510.747355053254-0.01192471312960.96792964317327.040966746236.610701597510.0700344061
226.7361128223-2.05251013771-6.100003782735.277950366662.914465465226.30446706694-0.7123300562240.497736430216-0.701752767048-0.06482221610620.1321198197730.710546140487-0.534615540401-0.2052256894580.4609130849030.6266986240540.0153801729625-0.08238226926820.7990741875910.03081551156780.614241625728.931359900433.48501891116.69918881062
237.81658317611-0.38975962974-2.96248284232.977975817890.6326357824043.17171261389-0.114697580396-0.9271363452190.7436436389030.5365140844360.482638032241-0.510062657934-1.06853818593-0.249100492794-0.1330482246081.104459407550.124059317458-0.07540264209430.7403984138950.01251298144130.94115542807514.936378530839.69714964257.11444500874
247.78800399671.716145116550.3157993667365.79252742756-5.977633332687.254068779740.1921972451360.174120155833-0.582903128101-0.430483363515-0.3944265293590.1454799226070.8341594992150.6458088946440.1300574510810.89238970434-0.0408117759893-0.0437617805060.563250132783-0.0417157179510.73819138082818.217852983731.079435370410.1985109379
255.830464860833.363088466460.2611302751525.271744227222.421953181167.132055005920.300544053449-0.2129182603050.2739304814860.712500539268-0.7081491290141.34346750832-0.975966402965-0.2903051016140.1977692543041.279197076860.0624694753919-0.07798568390360.5775183274810.03318284864640.73390280686918.655166198437.122442531319.7053164483
266.74993944558-4.761756902762.111339795186.9106509721-6.42141997917.29013438301-0.2759171953110.36860502855-0.7027958925420.8806471019370.327502286122-0.9101104250930.4275331478930.932457041868-0.05365024033440.7548862935380.04456592649530.01457221786480.677859227890.07135037241090.69061789934727.447750745131.003536141411.8090095979
273.3953888875-0.1993589305020.3065021003094.73562773552-4.642244662354.555044290030.4713028330670.305262846235-0.1503166906350.548932632469-1.58550974969-0.934527211138-0.1644993388050.3577134814161.013647752741.00132053405-0.0356800981654-0.2297750631181.04700357746-0.01300193441410.98013344207430.668463529846.478118711210.6478998981
284.3012690184-2.406372860521.539457713588.7684453033-6.090597075614.307942962410.5395696990640.3839048259590.614446162755-0.877499106379-1.24015292637-0.6848983676651.343686238530.10017481970.7018837160410.9099126840040.0736452682285-0.1443515553410.945882776553-0.03905523399950.78422301930931.63775599923.169012917117.7695769604
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 381 through 484 )BA381 - 4841 - 104
22chain 'B' and (resid 485 through 539 )BA485 - 539105 - 159
33chain 'B' and (resid 540 through 592 )BA540 - 592160 - 212
44chain 'C' and (resid 1 through 8 )CB1 - 81 - 8
55chain 'C' and (resid 9 through 17 )CB9 - 179 - 17
66chain 'C' and (resid 18 through 24 )CB18 - 2418 - 24
77chain 'C' and (resid 25 through 32 )CB25 - 3225 - 32
88chain 'C' and (resid 33 through 39 )CB33 - 3933 - 39
99chain 'C' and (resid 40 through 73 )CB40 - 7340 - 73
1010chain 'C' and (resid 74 through 83 )CB74 - 8374 - 83
1111chain 'C' and (resid 84 through 100 )CB84 - 10084 - 100
1212chain 'C' and (resid 101 through 106 )CB101 - 106101 - 106
1313chain 'C' and (resid 107 through 118 )CB107 - 118107 - 118
1414chain 'A' and (resid 382 through 425 )AC382 - 4251 - 44
1515chain 'A' and (resid 426 through 530 )AC426 - 53045 - 149
1616chain 'A' and (resid 531 through 544 )AC531 - 544150 - 163
1717chain 'A' and (resid 545 through 586 )AC545 - 586164 - 201
1818chain 'D' and (resid 1 through 8 )DD1 - 81 - 8
1919chain 'D' and (resid 9 through 24 )DD9 - 249 - 24
2020chain 'D' and (resid 25 through 32 )DD25 - 3225 - 32
2121chain 'D' and (resid 33 through 39 )DD33 - 3933 - 39
2222chain 'D' and (resid 40 through 52 )DD40 - 5240 - 52
2323chain 'D' and (resid 53 through 60 )DD53 - 6053 - 60
2424chain 'D' and (resid 61 through 73 )DD61 - 7361 - 73
2525chain 'D' and (resid 74 through 83 )DD74 - 8374 - 83
2626chain 'D' and (resid 84 through 100 )DD84 - 10084 - 100
2727chain 'D' and (resid 101 through 109 )DD101 - 109101 - 109
2828chain 'D' and (resid 110 through 116 )DD110 - 116110 - 116

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