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- PDB-8ysh: MERS-CoV RBD in complex with nanobody Nb14 -

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Basic information

Entry
Database: PDB / ID: 8ysh
TitleMERS-CoV RBD in complex with nanobody Nb14
Components
  • Nb14
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / MERS-CoV nanobody Nb14
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to 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 / 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, 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 / 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
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spike glycoprotein
A: Nb14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3464
Polymers35,5382
Non-polymers8082
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint6 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.488, 58.488, 351.625
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
Components on special symmetry positions
IDModelComponents
11B-736-

HOH

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Components

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


Mass: 23059.074 Da / Num. of mol.: 1
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 Nb14


Mass: 12478.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia (bacteria)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 6000, 8% Ethylene glycol, 0.1 M Citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.99→87.91 Å / Num. obs: 43747 / % possible obs: 99.87 % / Redundancy: 24.9 % / Biso Wilson estimate: 48.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.5
Reflection shellResolution: 1.99→2.09 Å / Num. unique obs: 4239 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→38.11 Å / SU ML: 0.2126 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 2165 4.95 %
Rwork0.2288 41579 -
obs0.2293 43744 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.37 Å2
Refinement stepCycle: LAST / Resolution: 1.99→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 53 74 2619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022599
X-RAY DIFFRACTIONf_angle_d1.09193538
X-RAY DIFFRACTIONf_chiral_restr0.0701416
X-RAY DIFFRACTIONf_plane_restr0.0146449
X-RAY DIFFRACTIONf_dihedral_angle_d14.0506925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.34171370.32882707X-RAY DIFFRACTION99.68
2.03-2.080.33671230.3232735X-RAY DIFFRACTION99.86
2.08-2.140.28821320.28242681X-RAY DIFFRACTION100
2.14-2.20.29551500.27572707X-RAY DIFFRACTION99.97
2.2-2.270.2821460.2622716X-RAY DIFFRACTION99.97
2.27-2.350.2691510.26122732X-RAY DIFFRACTION99.9
2.35-2.450.27371460.27432732X-RAY DIFFRACTION99.93
2.45-2.560.29061450.27082723X-RAY DIFFRACTION99.79
2.56-2.70.29171450.26882728X-RAY DIFFRACTION99.97
2.7-2.860.31641360.26822770X-RAY DIFFRACTION99.9
2.86-3.090.29561520.27372795X-RAY DIFFRACTION99.9
3.09-3.40.26511450.25492768X-RAY DIFFRACTION99.93
3.4-3.890.2761410.23022839X-RAY DIFFRACTION99.93
3.89-4.890.16711480.18322885X-RAY DIFFRACTION100
4.9-38.110.20651680.20033061X-RAY DIFFRACTION99.75
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)
10.4584176813970.2615682530360.832191757311.056114270220.5658335801752.02175349405-0.1372231130360.24258853306-0.08904122754740.4027384122740.216230543288-0.227232363147-0.07739757310230.674816216424-0.1095629718820.4687084926050.0391191158163-0.08982289867120.9912393232320.1154899227090.60576380089828.140113707821.5738144085-15.1996951821
22.183554299830.7371505421643.318498649413.665130309041.815087360515.32017504925-0.014427967001-0.264439283869-0.03580661331610.617124418511-0.005567888347570.2557472079930.376008565429-0.6889535448070.06569305608710.5126086908690.09224955183880.05956709830151.054834176310.1351018937960.468174938715.899993071517.445315091-16.3521741661
32.899073784712.00560258799-0.7008594349466.5309217474-1.025928306413.94914953762-0.0587174960845-0.082657379503-0.2496012999370.5453791836940.02622246900510.0417985414820.54668186521-0.08372864530410.08990263356050.2685660572140.06187679628380.02226383038911.08260693270.1549402301450.48489866526213.86484202587.00379379356-23.5270572076
40.572742077329-0.05371727336181.016966818123.23261946879-0.9429559651652.582809939090.0157945916270.257913148569-0.118690130084-0.1846000912930.3391837113330.2973072337290.525322629023-0.148852551408-0.4036740004240.3403189581340.0227381591299-0.01132601532141.108336628550.1286958941740.68397707428211.5534977838-0.27731262133-28.5794536334
51.93495096185-0.2988803610962.619282103462.7992291375-0.5463904226277.23922192836-0.4489702706950.3812847983220.2135538395630.3361359645760.375373291651-0.351587410719-0.4338581428730.2257227417340.01218390302180.4176381179770.0688839450301-0.03324690485681.077520528880.09874366824980.5334639966221.334954543121.8703009158-22.2621337712
67.443852052822.67332638073-5.638281594372.31139500066-3.123143447575.76014027364-0.0604454659927-1.49912875095-0.4494946396271.6549136174-0.190286881106-1.66998208683-0.7309878282970.177795312910.3817434786960.8988134389230.0540028664503-0.2933139926081.4300518127-0.1245725928440.85243221979335.93419617721.4472937734-2.20596806212
72.608785589062.21167499074-1.510440376152.63416469855-1.571490337582.83449099508-0.05487312185810.274787882978-0.447461096609-0.0457227555151-0.554166680361-0.97305303270.231418900284-0.02059579566350.5741273087040.353952241103-0.01235571768680.06696245974351.160315295520.1080311376580.83806990616135.3433591637.74311673608-46.7752151805
82.59524444569-2.762620747420.5307948128173.5854930985-0.1390335850440.3998767328240.04463811423230.8468633941220.374412099929-0.595520747197-0.37994940834-0.187499600991-0.347730034156-0.3300903841140.2625774950310.4256505371310.104826368493-0.07438365389251.233999270850.2232991651710.67477796266825.448802204326.1215252547-58.1248958689
95.6496590811-1.428672627630.4857376221287.09105428633-2.882696386194.21494312922-0.02427513061430.472407201914-0.606533674542-0.364042231034-0.210686738914-0.6702303424040.3499706461770.09608606466570.2779408758840.3402139489080.04286214666820.04144459621221.421866392610.1555070285340.55743020324428.179494002711.9655475801-53.6244739346
100.5652928074050.392989205673-0.9325068948412.538200317860.06141258966972.311213344980.059506507958-0.11208453479-0.3717664379250.0874816657674-0.130040083272-0.4553653859020.00572677884890.143326405610.06320675639020.302974407287-0.101974583202-0.0585008995461.21320579940.1310116393110.71048834691128.233931937411.5736565942-43.5098631288
113.040263701523.11180911360.5577512868959.237737088771.335553064832.01784131310.004954744962460.0679757793804-0.2290577317820.2714819166790.0734916896077-0.37130392166-0.2105842758090.396818598332-0.1228109007390.312594136919-0.043267389792-0.03466587416911.131474665650.1548841164430.59601059334423.078942467915.0794853552-40.8382808184
122.289558298-0.02921113109480.8235717119521.18717917473-0.008411215985560.3811602506150.04825452467570.3933306966310.0451087303552-0.165101912173-0.04182878554130.4200771142060.118924274094-0.0438216007160.1354527360270.126480419052-0.139634220716-0.01617587598261.356994826970.1310587375390.6908073178417.129309072611.5589373712-46.7957967239
133.048363398780.3841273741570.4684607577411.21622350185-0.6331960347180.4845747621960.1020405279660.201492233165-0.03344802290460.0276676832655-0.3035179015170.01870190764590.006836364982740.1653175880440.128038993320.3251002582550.03039862943590.01632809330561.271061938420.09971579950180.58498539334527.478268846514.8231470242-46.9382835764
145.77219178854-0.172574084220.1663601664053.21562266042.324623740042.74315737969-0.01560849041410.4898263858960.819040916672-0.202268482169-0.351394157766-0.0340404304554-0.2876534649730.03024083570830.2694204276250.3728230862950.0271396692510.01182105066131.433309807460.204404392880.70531682869429.450922867427.2736995012-53.3808094693
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 439 )BA381 - 4391 - 59
22chain 'B' and (resid 440 through 484 )BA440 - 48460 - 104
33chain 'B' and (resid 485 through 528 )BA485 - 528105 - 148
44chain 'B' and (resid 529 through 562 )BA529 - 562149 - 182
55chain 'B' and (resid 563 through 576 )BA563 - 576183 - 196
66chain 'B' and (resid 577 through 589 )BA577 - 589197 - 209
77chain 'A' and (resid 1 through 7 )AF1 - 71 - 7
88chain 'A' and (resid 8 through 17 )AF8 - 178 - 17
99chain 'A' and (resid 18 through 24 )AF18 - 2418 - 24
1010chain 'A' and (resid 25 through 44 )AF25 - 4425 - 44
1111chain 'A' and (resid 45 through 51 )AF45 - 5145 - 51
1212chain 'A' and (resid 52 through 72 )AF52 - 7252 - 72
1313chain 'A' and (resid 73 through 109 )AF73 - 10973 - 109
1414chain 'A' and (resid 110 through 116 )AF110 - 116110 - 116

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