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- PDB-8yk4: Structure of SARS-CoV-2 RBD and antibody NT-108 -

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Basic information

Entry
Database: PDB / ID: 8yk4
TitleStructure of SARS-CoV-2 RBD and antibody NT-108
Components
  • Spike protein S1
  • antibody NT-108, single chain Fv fragment
KeywordsVIRAL PROTEIN / SARS-CoV-2 / spike / RBD / antibody / IgG / scFv
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, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAnraku, Y. / Kita, S. / Onodera, T. / Sato, A. / Tadokoro, T. / Adachi, Y. / Ito, S. / Suzuki, T. / Sasaki, J. / Shiwa, N. ...Anraku, Y. / Kita, S. / Onodera, T. / Sato, A. / Tadokoro, T. / Adachi, Y. / Ito, S. / Suzuki, T. / Sasaki, J. / Shiwa, N. / Iwata, N. / Nagata, N. / Kazuki, Y. / Oshimura, M. / Sasaki, M. / Orba, Y. / Suzuki, T. / Sawa, H. / Hashiguchi, T. / Fukuhara, H. / Takahashi, Y. / Maenaka, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20fk0108298 Japan
Japan Agency for Medical Research and Development (AMED)JP20ae0101047 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101093 Japan
CitationJournal: To Be Published
Title: Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108
Authors: Anraku, Y. / Tadokoro, T. / Suzuki, T. / Sasaki, J. / Hashiguchi, T. / Kita, S. / Shiwa, N. / Iwata, N. / Nagata, N. / Suzuki, T. / Kazuki, Y. / Fukuhara, H. / Oshimura, M. / Sato, A. / ...Authors: Anraku, Y. / Tadokoro, T. / Suzuki, T. / Sasaki, J. / Hashiguchi, T. / Kita, S. / Shiwa, N. / Iwata, N. / Nagata, N. / Suzuki, T. / Kazuki, Y. / Fukuhara, H. / Oshimura, M. / Sato, A. / Sasaki, M. / Orba, Y. / Sawa, H. / Maenaka, K.
History
DepositionMar 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody NT-108, single chain Fv fragment
C: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)54,0192
Polymers54,0192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-9 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.152, 149.641, 253.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody antibody NT-108, single chain Fv fragment


Mass: 29873.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein Spike protein S1


Mass: 24145.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A7U3DZD0
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: 4.84 Å3/Da / Density % sol: 74.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M CHES pH9.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48.35 Å / Num. obs: 17765 / % possible obs: 99.6 % / Redundancy: 9.4 % / Biso Wilson estimate: 59.17 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.7
Reflection shellResolution: 3.2→3.42 Å / Num. unique obs: 3153 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
XDS1.18_3845data reduction
Aimless1.18_3845data scaling
PHENIX1.20.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.35 Å / SU ML: 0.4561 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 861 4.85 %
Rwork0.2429 16877 -
obs0.244 17738 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.12 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 0 0 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00113258
X-RAY DIFFRACTIONf_angle_d0.40144426
X-RAY DIFFRACTIONf_chiral_restr0.0417476
X-RAY DIFFRACTIONf_plane_restr0.0032570
X-RAY DIFFRACTIONf_dihedral_angle_d14.98491151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.40.34721510.32232735X-RAY DIFFRACTION98.94
3.4-3.660.33011580.28862764X-RAY DIFFRACTION99.19
3.66-4.030.30331380.26372761X-RAY DIFFRACTION99.18
4.03-4.610.20831330.20352810X-RAY DIFFRACTION99.53
4.61-5.810.23241460.20062817X-RAY DIFFRACTION99.4
5.81-48.350.24871350.24272990X-RAY DIFFRACTION99.4
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)
12.420552925413.07010731984-0.6194993880654.34039954270.09804184086471.905610984120.079161063864-0.407082276341-1.478886783420.6186737055280.1178652484650.2250226832520.3287653806760.130904033637-0.1512318110310.4418659078240.076066104452-0.03224518028090.3525765607420.1165285966710.9579614755753.6857286436211.137752054574.6013633283
24.148656760270.8820844100531.316572374855.178938454330.3033206126684.983232117090.223620700783-0.308359304496-0.496141630880.5501059861570.06162465108640.9998010176230.244560691689-0.298932308813-0.3550323926640.524531501064-0.05656889682530.09496540677270.3014910152150.04544449948860.662695501804-3.0470438031916.496286892476.6268337647
36.853470256395.03329711498-0.395548576294.491289117010.6579223971841.18145959506-0.437494361768-0.0234459189385-0.636259449965-0.6136761415560.1685570822850.544979348353-0.1001820762950.07718859812910.2607488416790.3938268787820.0839537533397-0.1012508024920.3473719637370.1226535651371.0419734851-0.27016875376613.473049683570.1908084516
41.60305554071-1.833770323050.3092048501545.89980492591.701312327281.27873378451-0.09979334490340.5361002567680.634913051369-0.3736523674130.126573522461-0.4924280588930.381956541703-0.3413844710.06761270744640.368533095390.0623250029534-0.04918447767580.4406776490050.05291364116150.3454367018291.4940455145429.633668674454.9982475231
55.026663149350.377348091145-0.5803929518961.03697668007-0.4878871611124.474138307310.0149381416483-0.07028387619060.131637850533-0.3131096539860.0520342710450.0231740255872-0.04957944402760.137090867492-0.08715786321680.372465034114-0.00503192049588-0.053712058240.161287255207-0.0104831149990.4424279138088.3351239938134.349934611164.3076734516
62.5397101331-0.920590709121-1.822223682412.496032274833.80111103099.319730365040.02633659568670.0662636745174-0.0750284991822-0.02934004146330.110781107395-0.08534874896880.274828630634-0.0362513349767-0.221987473770.344402228499-0.003407343394810.01402550021320.1775878294580.05069747692850.5082494639685.4784108365326.725052994960.8943810405
76.04699502151.11388919342-0.1922028294618.75192782159-0.9905611614881.99721978792-0.23113790709-1.37135329270.593710637121-0.3484666171570.9484008798660.667969209853-0.4519653263570.530624202365-0.7746002496450.7937812269730.192129756766-0.0821167570170.8653794203-0.123335447260.50739647706-10.104722840336.551499799599.429407868
82.74818302907-1.39186674044-0.8751459766843.63507375078-2.051404881793.07262517998-0.574317639786-0.976743873693-1.360647428031.15966598605-0.4008068068810.872661126806-0.44960961210.01450633668760.7822584324991.003390685730.002013904201820.3661888338711.67442207516-0.4439635548790.840591568065-12.078126288238.7110753323112.543075364
97.80966660636-4.471928514991.603966181544.00848949844-0.08646493985080.8078318290660.396444969209-1.681146502690.3335498602361.76559887340.7175702923132.3606438710.327843793703-1.25458817875-0.9518852837061.46881834895-0.1397453349330.6071236806211.310598518720.4004793590311.51001757367-15.789187193923.7970536213108.156244051
103.64657385113-1.20719717467-4.535035448990.4089742798591.48186131345.67055781735-0.976445658239-1.669739180530.4828222230420.2121937323460.7079181776530.01589039816210.1301526560221.512993109120.3090781689141.37557553804-0.152735714534-0.1241584325211.734585380510.005038606790620.732740272111-10.113391756927.0864000583118.878453049
116.663170942120.98291352777-0.4550062470895.635566044961.519444515786.77584308485-0.45126282493-0.942111268048-0.2563291908380.753958641283-0.0750879090632-0.2309526211340.1237977308760.54455980640.4692571283970.94376968873-0.007059464275470.01086403771681.144023854160.1530594009690.484737593427-4.4413020471627.5286240049100.556485849
122.43026603080.664762172956-0.8404102268273.818443754650.9645668321880.685754553906-0.19198841566-0.835062685723-0.1924864529450.89001946773-0.01120244703260.2217669064140.242107807988-0.3639537829570.1723087332550.7317382722220.04196199440920.1218448109940.9824559120940.1174628445520.438933005449-4.198500415227.479080085598.4700709748
133.756809114550.328841232853-2.554284286223.28925397158-0.5046449597776.11840769642-0.217703598045-0.6870130914070.07896815225620.5342920422110.1939696358960.0308813384171-0.5296824350660.4925825789660.01522575904920.5597811723080.0809587665845-0.1552002091970.5076164656470.007185912478260.5834574629477.837945190431.928564056788.9695360946
142.31750203139-0.0860253559482-0.6172145308930.03051245297120.3144289173952.975309346740.17706768347-0.6150467133140.1512261028141.295571519850.0374374468706-0.108857461842-0.140746432828-0.0252343920039-0.1490864973781.26688588926-0.02203923635780.03622665767451.04023325606-0.09134970247480.368576985888-8.9137991495229.8362725724104.947241487
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 40 )AA3 - 401 - 38
22chain 'A' and (resid 41 through 77 )AA41 - 7739 - 75
33chain 'A' and (resid 78 through 107 )AA78 - 10776 - 105
44chain 'A' and (resid 108 through 140 )AA108 - 140106 - 124
55chain 'A' and (resid 141 through 209 )AA141 - 209125 - 193
66chain 'A' and (resid 210 through 246 )AA210 - 246194 - 230
77chain 'C' and (resid 338 through 353 )CB338 - 3531 - 16
88chain 'C' and (resid 354 through 367 )CB354 - 36717 - 30
99chain 'C' and (resid 368 through 379 )CB368 - 37931 - 42
1010chain 'C' and (resid 380 through 394 )CB380 - 39443 - 52
1111chain 'C' and (resid 395 through 409 )CB395 - 40953 - 67
1212chain 'C' and (resid 410 through 451 )CB410 - 45168 - 109
1313chain 'C' and (resid 452 through 502 )CB452 - 502110 - 160
1414chain 'C' and (resid 503 through 525 )CB503 - 525161 - 178

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