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- PDB-8sk5: Crystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to... -

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Basic information

Entry
Database: PDB / ID: 8sk5
TitleCrystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to the spike receptor binding domain
Components
  • Spike protein S1
  • anti-SARS-CoV-2 receptor binding domain VHH
KeywordsANTIVIRAL PROTEIN / VHH / Complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsNoland, C.L. / Pande, K. / Zhang, L. / Zhou, H. / Galli, J. / Eddins, M. / Gomez-Llorente, Y.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Sci Rep / Year: 2023
Title: Discovery and multimerization of cross-reactive single-domain antibodies against SARS-like viruses to enhance potency and address emerging SARS-CoV-2 variants.
Authors: Hollingsworth, S.A. / Noland, C.L. / Vroom, K. / Saha, A. / Sam, M. / Gao, Q. / Zhou, H. / Grandy, D.U. / Singh, S. / Wen, Z. / Warren, C. / Ma, X.S. / Malashock, D. / Galli, J. / Go, G. / ...Authors: Hollingsworth, S.A. / Noland, C.L. / Vroom, K. / Saha, A. / Sam, M. / Gao, Q. / Zhou, H. / Grandy, D.U. / Singh, S. / Wen, Z. / Warren, C. / Ma, X.S. / Malashock, D. / Galli, J. / Go, G. / Eddins, M. / Mayhood, T. / Sathiyamoorthy, K. / Fridman, A. / Raoufi, F. / Gomez-Llorente, Y. / Patridge, A. / Tang, Y. / Chen, S.J. / Bailly, M. / Ji, C. / Kingsley, L.J. / Cheng, A.C. / Geierstanger, B.H. / Gorman, D.M. / Zhang, L. / Pande, K.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: anti-SARS-CoV-2 receptor binding domain VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8913
Polymers44,3202
Non-polymers5711
Water2,828157
1
A: Spike protein S1
hetero molecules

B: anti-SARS-CoV-2 receptor binding domain VHH


Theoretical massNumber of molelcules
Total (without water)44,8913
Polymers44,3202
Non-polymers5711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z+1/31
Buried area1830 Å2
ΔGint3 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.903, 93.903, 121.386
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Protein anti-SARS-CoV-2 receptor binding domain VHH


Mass: 18224.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M Sodium malonate pH 6.0, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.011→81.322 Å / Num. obs: 29582 / % possible obs: 70.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 42.07 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.024 / Rrim(I) all: 0.075 / Net I/σ(I): 18.3 / Num. measured all: 294120
Reflection shellResolution: 2.011→2.216 Å / % possible obs: 14.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.999 / Num. measured all: 10152 / Num. unique obs: 1476 / Rpim(I) all: 0.405 / Rrim(I) all: 1.08 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.011→36.23 Å / SU ML: 0.2173 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 1470 4.97 %
Rwork0.1832 28102 -
obs0.1845 29572 70.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.94 Å2
Refinement stepCycle: LAST / Resolution: 2.011→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 38 157 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242640
X-RAY DIFFRACTIONf_angle_d0.56483591
X-RAY DIFFRACTIONf_chiral_restr0.0427388
X-RAY DIFFRACTIONf_plane_restr0.0037469
X-RAY DIFFRACTIONf_dihedral_angle_d5.0638390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.011-2.080.4946120.3322139X-RAY DIFFRACTION4.05
2.08-2.150.2527250.2862504X-RAY DIFFRACTION14.17
2.15-2.240.3475490.27021035X-RAY DIFFRACTION28.75
2.24-2.340.24940.26641726X-RAY DIFFRACTION48.9
2.34-2.460.29811630.2782861X-RAY DIFFRACTION80.45
2.46-2.620.28311930.24983564X-RAY DIFFRACTION99.97
2.62-2.820.25711960.22833577X-RAY DIFFRACTION100
2.82-3.10.2281740.22053616X-RAY DIFFRACTION100
3.1-3.550.21311960.18063611X-RAY DIFFRACTION100
3.55-4.470.18921660.14793681X-RAY DIFFRACTION99.97
4.47-36.230.16642020.15183788X-RAY DIFFRACTION99.95
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)
10.3163376519540.8254102616460.3417355472440.711740028960.3309448462780.5762865364350.1744509072470.61551585280.278992369002-0.403308598881-0.209090421134-0.576306926047-0.01036556856630.6340940170110.0001527206902640.3982862980120.0217837966350.004066751381280.6223837226620.1113280602580.491265745186.72328145626-35.16156597142.59043365965
20.366422713878-0.6735351793590.251811652870.154269216358-0.1713675096990.4423218953760.02483360047930.1219214866330.179001545193-0.4460203905670.0207117412691-0.955242399938-0.3802681524410.758606494587-7.01240551705E-80.506377138269-0.08155567645-0.02396485718290.9108540225690.10773781340.65360650171118.0968635999-33.90748106198.12968586139
31.771719992631.548760740480.5555825730970.836599168767-0.9454200438192.43243119293-0.0106513117878-0.03684581149290.2941773325820.223947788356-0.139836780474-0.409712598945-0.2013128341180.678172509864-3.23049868448E-80.367280555139-0.0525564581575-0.1063255737760.6203449463780.05248740010570.3992803190219.56644781858-32.774122188714.4426601186
43.70680559827-0.2270652775291.420743668352.475859353350.4437110533762.09047697746-0.2076229320860.212401069230.5360163446790.0617063427699-0.0146538222798-0.143716931608-0.3453684282310.1314515776583.27774143988E-80.361937873401-0.032317554795-0.06447773175210.3599248209780.05026394527230.38555934881-2.99919098748-27.7628444711.0620183806
50.940598342942-0.1733977799260.4606635000940.506358706621-1.089372193050.4234777804310.0425166859864-0.07284391361440.3627327853360.188938880959-0.0657094948633-0.0589762530969-0.4306734142060.06132880533156.29133207359E-80.4952900648370.0375412819366-0.07512085983560.478697459574-0.04261475595020.43704165504-22.6898651318-23.37607082098.1625560992
60.0004776662743190.06112698130930.03975332024140.0545116956318-0.0490236396918-0.0847649330646-0.4649155096440.143673661071.211185485790.305109857108-0.08199774952480.214178005805-0.956727347607-0.191206732001-1.74776259759E-60.714578224463-0.125025718622-0.1818768629280.4875430284920.1240907417830.9109002742440.429915013959-12.90541998766.13590129585
72.346989901020.287281400072-0.1560259999120.3725627897561.079508344272.0110473086-0.0901713707350.038914213621-0.01052353244930.100764637207-0.0476336621963-0.5546208590190.3048354125170.6267957518336.62888229823E-70.3586248725570.0115635082769-0.05805717460980.591629187250.09731829455580.41383645303410.5009882062-39.886780000811.470766637
80.200455298864-0.0513793056065-1.215841930441.97936645101-0.4594727648461.578537793570.0908413932127-0.33404419282-0.741878401330.275134289728-0.0194490927451-0.07798192825610.561163966582-0.0538152983274-1.46250003377E-60.5219759639320.01936085366980.05381275116880.377390953746-0.1606930463780.553348400184-14.4777568148-58.7368767327-3.89122747732
90.838238822805-0.0909949180642-0.1992742576350.9646630462611.166189733040.4504295242340.142882305406-0.0294848008007-0.5620288015480.319351330858-0.0579636489249-0.06732084843630.6948172646930.306227451973-4.61404240079E-70.4681600076640.00541966276802-0.0148652251780.3904954691480.006338362807750.480230650308-8.83320998005-54.74465080232.96679973593
100.7385601378670.1860099423880.06431259838330.9395788947510.2565238291560.134900649795-0.14780455540.5027694390690.0254750418396-0.5217959512820.111232367598-0.102624172540.1764194438880.6342514813497.44017089621E-70.384472712769-0.003619278810990.03227827263520.554029813631-0.02398547803440.415512334767-9.34278123594-46.9119115429-7.46605598031
110.09564515683210.0201184024936-0.1237681865570.09486907196870.0665299805341-0.04206798859490.257778312519-1.298540533970.001675720884620.980840457163-0.1843443354470.0534306580610.27322139341-0.0608059423584-1.22098946122E-60.625441423492-0.04166063481220.0275502690390.5664441213880.01588213372780.336659419681-8.75801616373-46.625956135316.8716047639
121.280735186740.6508842879350.2788848524950.6403693270651.842277173461.001024359160.112823300008-0.0847897992405-0.06560224520980.271609725338-0.1263338079980.157015936822-0.1288807826750.01957188805553.18337937689E-70.368097908758-0.022440987430.03306100049360.384332209593-0.03904631203860.334383460016-17.2226498195-46.35360069082.30501054377
130.466301720223-0.0195169012971-0.4199502707450.4937300123260.3685388257280.3162345632130.159017826786-0.351884072036-0.4188116581540.580140507279-0.181917782831-0.3635014610560.840527317830.376677154219-0.01134703281890.64981015340.02704690397970.001680468587980.5599091433350.04061431117020.530981778394-14.1358056712-56.67149697316.56000131567
140.5412768666090.1680776359820.05996036253080.4627821974460.4801184332621.30432190941-0.0532712339450.2310855782-0.147652470540.102775999703-0.1483228110710.04440491073540.1802414562590.100294634614-1.13374054839E-70.3635031365520.0189351285580.02817086171870.372581449759-0.02063244075350.354356633463-10.4991757723-47.71839794-0.934076077237
150.6565409907740.144185136975-1.167995605131.799519669940.3173919971611.128674531190.01139784842840.288407326152-0.39875768453-0.03972309830080.0357962528658-0.04577284754560.3018634283540.382420855927.53634000153E-70.3633540091280.08766174186710.0121897746450.452511354156-0.1085371657690.379847764252-8.39518359984-53.0315073652-6.00722387007
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 333 through 358 )AA333 - 3581 - 26
22chain 'A' and (resid 359 through 375 )AA359 - 37527 - 43
33chain 'A' and (resid 376 through 409 )AA376 - 40944 - 77
44chain 'A' and (resid 410 through 469 )AA410 - 46978 - 137
55chain 'A' and (resid 470 through 494 )AA470 - 494138 - 162
66chain 'A' and (resid 495 through 506 )AA495 - 506163 - 174
77chain 'A' and (resid 507 through 527 )AA507 - 527175 - 195
88chain 'B' and (resid 1 through 17 )BE1 - 171 - 17
99chain 'B' and (resid 18 through 39 )BE18 - 3918 - 39
1010chain 'B' and (resid 40 through 51 )BE40 - 5140 - 51
1111chain 'B' and (resid 52 through 62 )BE52 - 6252 - 62
1212chain 'B' and (resid 63 through 78 )BE63 - 7863 - 78
1313chain 'B' and (resid 79 through 88 )BE79 - 8879 - 88
1414chain 'B' and (resid 89 through 114 )BE89 - 11489 - 114
1515chain 'B' and (resid 115 through 135 )BE115 - 135115 - 132

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