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- PDB-7e5o: Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193 -

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Basic information

Entry
Database: PDB / ID: 7e5o
TitleCrystal structure of SARS-CoV-2 RBD in complex with antibody NT-193
Components
  • NT-193 Heavy chain
  • NT-193 Light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / spike / IgG
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / membrane / identical protein binding / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKita, S. / Onodera, T. / Adachi, Y. / Moriayma, S. / Nomura, T. / Tadokoro, T. / Anraku, Y. / Yumoto, K. / Tian, C. / Fukuhara, H. ...Kita, S. / Onodera, T. / Adachi, Y. / Moriayma, S. / Nomura, T. / Tadokoro, T. / Anraku, Y. / Yumoto, K. / Tian, C. / Fukuhara, H. / Suzuki, T. / Tonouchi, K. / Sasaki, J. / Sun, L. / Hashiguchi, T. / Takahashi, Y. / Maenaka, K.
CitationJournal: Immunity / Year: 2021
Title: A SARS-CoV-2 antibody broadly neutralizes SARS-related coronaviruses and variants by coordinated recognition of a virus-vulnerable site.
Authors: Onodera, T. / Kita, S. / Adachi, Y. / Moriyama, S. / Sato, A. / Nomura, T. / Sakakibara, S. / Inoue, T. / Tadokoro, T. / Anraku, Y. / Yumoto, K. / Tian, C. / Fukuhara, H. / Sasaki, M. / ...Authors: Onodera, T. / Kita, S. / Adachi, Y. / Moriyama, S. / Sato, A. / Nomura, T. / Sakakibara, S. / Inoue, T. / Tadokoro, T. / Anraku, Y. / Yumoto, K. / Tian, C. / Fukuhara, H. / Sasaki, M. / Orba, Y. / Shiwa, N. / Iwata, N. / Nagata, N. / Suzuki, T. / Sasaki, J. / Sekizuka, T. / Tonouchi, K. / Sun, L. / Fukushi, S. / Satofuka, H. / Kazuki, Y. / Oshimura, M. / Kurosaki, T. / Kuroda, M. / Matsuura, Y. / Suzuki, T. / Sawa, H. / Hashiguchi, T. / Maenaka, K. / Takahashi, Y.
History
DepositionFeb 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _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
H: NT-193 Heavy chain
L: NT-193 Light chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0654
Polymers73,6413
Non-polymers4241
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-25 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.073, 106.886, 148.074
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody NT-193 Heavy chain


Mass: 26200.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody NT-193 Light chain


Mass: 23295.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: 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
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: 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.: 1
Source method: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.89 Å3/Da / Density % sol: 74.86 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 10% (w/v) PEG 8000, 8% (w/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→45.1 Å / Num. obs: 33546 / % possible obs: 99.88 % / Redundancy: 6.8 % / Biso Wilson estimate: 60.15 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.2054 / Rpim(I) all: 0.08524 / Rrim(I) all: 0.2228 / Net I/σ(I): 5.75
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 3306 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7jmp

7jmp


Resolution: 2.8→45.1 Å / SU ML: 0.3745 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 1661 4.95 %
Rwork0.2262 31861 -
obs0.2277 33522 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 28 17 4833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734938
X-RAY DIFFRACTIONf_angle_d0.9826718
X-RAY DIFFRACTIONf_chiral_restr0.0581744
X-RAY DIFFRACTIONf_plane_restr0.0052857
X-RAY DIFFRACTIONf_dihedral_angle_d16.73741753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.39011460.35952602X-RAY DIFFRACTION99.85
2.88-2.980.35841250.31422608X-RAY DIFFRACTION99.93
2.98-3.080.31981500.29072600X-RAY DIFFRACTION99.96
3.08-3.210.29861220.27582644X-RAY DIFFRACTION99.96
3.21-3.350.33741400.27572621X-RAY DIFFRACTION100
3.35-3.530.30321220.26222640X-RAY DIFFRACTION99.78
3.53-3.750.2831320.23882637X-RAY DIFFRACTION100
3.75-4.040.24871640.22032626X-RAY DIFFRACTION99.89
4.04-4.440.19691410.18672655X-RAY DIFFRACTION100
4.44-5.090.18411400.16942687X-RAY DIFFRACTION100
5.09-6.40.24851380.1952707X-RAY DIFFRACTION99.96
6.41-45.10.24731410.21792834X-RAY DIFFRACTION99.63
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)
18.56773331882-0.091125532749.252255478194.24517727311-1.656454786082.098172245270.933023364628-0.0610947754218-1.31353640596-0.288570869425-0.301765648431-0.1864443783241.24208239355-0.170866603241-0.6537498447420.838845950581-0.01633644789060.07909899132050.699663209806-0.05581149889510.373327128608-21.9480993932-1.521518347216.87001321503
26.091771257471.322855572821.547275593915.220673207920.2473503133419.62782477940.0109461671429-0.0359664785705-0.278891912970.2867659029510.107166491871-0.05817984807020.487581977798-0.116811441678-0.1264843457370.383863943506-0.02082023475140.0649470503260.247418841086-0.04747169865960.332729207688-18.9612842737.5621631205212.6395401101
30.7114547020691.051993632451.633314773234.352168979792.770936876643.7217749478-0.079570824258-0.0238023229496-0.2791386102430.3000459602860.273735834835-0.1335340774860.102602468510.00229490531529-0.2016351604570.437779301466-0.01849074843660.1139810227030.399611122452-0.01740682923070.347596870688-18.96812613165.88991098514.7266093544
49.7668711268-2.97501739361-0.5891430821428.840990779437.310121049056.440082853540.3796243713721.363248272061.22672844234-1.988822094030.465474839401-0.353456020648-0.114720638003-0.507962883904-0.8061455374140.8073643619510.128832280331-0.1043697660230.5381110427490.03458664110350.51000153765-27.8663340178-4.16827643977-34.2124287624
57.47465455906-2.11515228509-2.540787821288.147885461725.135303696818.678978131640.104120889619-0.0284535697511-0.224172486624-0.2149650971710.143538340236-0.2064682912880.4703751957920.235191124756-0.3172464218250.403646896679-0.00791910464309-0.009423978703730.3202764263320.01302272882010.29825109736-23.5326047518-6.31756841106-23.9147380397
65.717376182341.68493521363-4.743958638718.059219898070.7398536414324.538143444150.1512054068410.0717224424372-0.458945959494-0.2596062678430.1053522737120.1530183861322.2075922699-0.739609459407-0.2576402242070.49198093812-0.0944524419416-0.064582819590.39453793162-0.03820151784030.440145984901-29.4892576793-13.0932182748-25.9327407946
72.7815637117-0.0436763810066-1.620611309472.368374782851.512012667899.974909035070.01159914473020.402666778723-0.0481295867199-0.5232614737180.339399657417-0.512183793178-0.4458370491030.496258235426-0.3631989799930.379681134-0.1134152929020.09062483401810.455383201621-0.09615238706830.457277599229-5.5195416131317.4262752995-2.61441031537
80.324563583564-0.42418078314-1.820100390.5762298479222.165635579091.998636777750.2378276513910.08020037783910.619807974704-0.5528511751180.588635879373-0.467084858592-0.4350824849550.290718129055-0.8237698472630.681046413331-0.1948025155870.169785138740.655969847775-0.1327355353930.502811913073-7.4969473258912.0131817489-24.093617842
99.690011651091.787245394421.804949407584.356699969090.9718893520265.63416397531-0.170226971483-0.258571064293-0.0023071738426-0.8482223474290.172136532829-0.270297350427-0.5400628027870.238808206672-0.03836357453660.6167952713150.04373560633320.09216183132880.33873862769-0.02745949264950.277253712366-28.63280604626.72814680506-29.8736932543
105.303347930550.00806262657383-0.4201353977630.958533025672-0.7508402345051.990064802410.158767250408-0.07890090657260.107897441589-0.2807037558510.06735190756890.0414265606106-0.2409275930760.0839432832471-0.2305282916520.695348822937-0.03656022962260.02914967468820.413932188668-0.08728245236150.371072746872-27.25319336548.35780939939-30.0564819253
115.374782607311.31536638639-3.283019579410.62548615222-1.816479690795.503800881340.310733498668-0.839436540150.5023407089731.03512911517-0.08869545545610.174819633841-0.9173433495270.101576708536-0.2091299315231.02865891496-0.02895040378540.1491359512460.458580093218-0.05703156318860.484764533075-10.76266028831.473795924939.7338839848
126.803246049653.23506272429-8.104558476184.42982885397-5.310468082762.005861505721.20875778815-1.003900690240.1593754798070.555928692462-0.4930570023660.0978864209733-2.63685628140.277820806457-0.734181221951.71901650941-0.277993539544-0.222843360611.156809307430.1211824154440.731238516156-3.8012978203327.405224540951.5166960621
134.239721113940.974884218316-0.5057512527963.00608264842-0.7748994464724.140580065790.08112695006290.03245715129590.09049251653660.1660777928560.137909601847-0.211420917221-0.1808474373460.451142552047-0.1992320073630.489814478143-0.02540331063320.007304525834070.281215942932-0.09833063764050.335736267931-2.893777008928.582747129822.2179307522
148.027730145510.3252439264922.972673967452.31497063809-2.234402072467.22268323144-0.234069165442-0.3204261673950.4446214194590.263961994402-0.348383633475-0.0335040685845-1.02700010678-0.3223523155710.5986092597570.5190622686890.07448875293790.1104064050880.2517233341710.03283348120790.386901323857-10.597612959627.644543481631.1832878102
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 82 )HA18 - 8218 - 82
33chain 'H' and (resid 83 through 126 )HA83 - 12683 - 126
44chain 'H' and (resid 127 through 141 )HA127 - 141127 - 138
55chain 'H' and (resid 142 through 207 )HA142 - 207139 - 204
66chain 'H' and (resid 208 through 223 )HA208 - 223205 - 220
77chain 'L' and (resid 2 through 103 )LC2 - 1031 - 102
88chain 'L' and (resid 104 through 114 )LC104 - 114103 - 113
99chain 'L' and (resid 115 through 156 )LC115 - 156114 - 155
1010chain 'L' and (resid 157 through 214 )LC157 - 214156 - 213
1111chain 'A' and (resid 334 through 380 )C000E334 - 3801 - 47
1212chain 'A' and (resid 381 through 393 )C000E381 - 39348 - 60
1313chain 'A' and (resid 394 through 494 )C000E394 - 49461 - 161
1414chain 'A' and (resid 495 through 525 )C000E495 - 525162 - 188

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