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- PDB-8hes: Crystal structure of SARS-CoV-2 RBD and NIV-10 complex -

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Basic information

Entry
Database: PDB / ID: 8hes
TitleCrystal structure of SARS-CoV-2 RBD and NIV-10 complex
Components
  • NIV-10 Fab H-chain
  • NIV-10 Fab L-chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / virus / SARS-CoV-2 / RBD / spike / antibody / IgG / neutralizing antibody / complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMoriyama, S. / Anraku, Y. / Taminishi, S. / Adachi, Y. / Kuroda, D. / Higuchi, Y. / Kotaki, R. / Tonouchi, K. / Yumoto, K. / Suzuki, T. ...Moriyama, S. / Anraku, Y. / Taminishi, S. / Adachi, Y. / Kuroda, D. / Higuchi, Y. / Kotaki, R. / Tonouchi, K. / Yumoto, K. / Suzuki, T. / Kita, S. / Someya, T. / Fukuhara, H. / Kuroda, Y. / Yamamoto, T. / Onodera, T. / Fukushi, S. / Maeda, K. / Nakamura-Uchiyama, F. / Hashiguchi, T. / Hoshino, A. / Maenaka, K. / Takahashi, Y.
Funding support Japan, 10items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20fk0108516 Japan
Japan Agency for Medical Research and Development (AMED)JP 21fk0108465 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108298 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108534 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108534 Japan
Japan Agency for Medical Research and Development (AMED)JP19fk0108104 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108104 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05873 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05773 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Authors: Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki ...Authors: Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki / Taiyou Someya / Hideo Fukuhara / Yudai Kuroda / Tsukasa Yamamoto / Taishi Onodera / Shuetsu Fukushi / Ken Maeda / Fukumi Nakamura-Uchiyama / Takao Hashiguchi / Atsushi Hoshino / Katsumi Maenaka / Yoshimasa Takahashi /
Abstract: SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies ...SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: NIV-10 Fab H-chain
C: Spike protein S1
L: NIV-10 Fab L-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1484
Polymers73,9263
Non-polymers2211
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-29 kcal/mol
Surface area27530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.147, 101.113, 134.265
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 NIV-10 Fab H-chain


Mass: 26826.963 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: Hekistocarpa minutiflora (plant) / References: UniProt: P0DTC2
#3: Antibody NIV-10 Fab L-chain


Mass: 22954.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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
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.: 236 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.31 Å / Num. obs: 36935 / % possible obs: 98.15 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.062 / Rrim(I) all: 0.164 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 3145 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7eam

7eam


Resolution: 2.2→47.31 Å / SU ML: 0.2988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 1785 4.84 %
Rwork0.1962 35073 -
obs0.1983 36858 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 0 14 236 4991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784879
X-RAY DIFFRACTIONf_angle_d1.02426647
X-RAY DIFFRACTIONf_chiral_restr0.0631729
X-RAY DIFFRACTIONf_plane_restr0.008857
X-RAY DIFFRACTIONf_dihedral_angle_d13.47891721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.31591360.27892642X-RAY DIFFRACTION98.41
2.26-2.330.32641420.2512648X-RAY DIFFRACTION98.07
2.33-2.40.27311440.25232695X-RAY DIFFRACTION99.4
2.4-2.490.31420.24542677X-RAY DIFFRACTION98.53
2.49-2.590.37231370.24792502X-RAY DIFFRACTION92.96
2.59-2.70.3081410.23472671X-RAY DIFFRACTION98.91
2.7-2.850.24831390.21312699X-RAY DIFFRACTION99.23
2.85-3.020.24931440.20962707X-RAY DIFFRACTION99.27
3.03-3.260.26711280.20842763X-RAY DIFFRACTION99.59
3.26-3.590.2141190.18312741X-RAY DIFFRACTION99.13
3.59-4.10.22581310.17282663X-RAY DIFFRACTION95.52
4.11-5.170.19071270.14952809X-RAY DIFFRACTION99.86
5.17-47.310.19761550.19392856X-RAY DIFFRACTION97.35
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)
11.558315453980.794373615790.9320665550671.43084498060.3870844521631.973069800770.01997413284330.00366052982682-0.0349448705511-0.0139764881076-0.00782979678756-0.03591296679440.09014813420350.0605475129893-0.02613474923850.2222792945980.0234491030410.006848186815920.2524849883580.008519643072110.232881183759-11.1138848245-15.2734533458-13.1790708139
23.241761760720.4232236961060.7561711834884.93420463687-0.6060165029136.101895701690.08319975951570.2279440143590.3715505165470.0265314812666-0.3497021539560.105608898728-0.437664685671-0.2275535715820.26068362180.3119259283540.02217052413580.02295445725740.3888692865590.06178928608810.33329914332811.812822373714.7863754932-13.0409016533
35.467718211840.981050282891-1.381760362127.03208324567-2.075907548518.255778090450.289577654623-0.06944291173331.007937138910.424671603937-0.3856033932-0.0687375576285-1.68422945578-0.01515067330980.1588192862010.555341443999-0.00670044464108-0.03542058660810.3685540464510.04991471528850.51948915134714.3652419920.226200701-10.2247862074
46.875488789511.66168639745-1.725905608986.72693485613-1.876124832866.56544337172-0.4194167036380.375625971411-0.8664783539580.002076697799440.1047843501910.008465558641231.01565432218-0.2193573499030.2987470096080.460707997821-0.06034385526640.03196871330020.342978099052-0.1188527489960.311681304876-37.7574661406-51.1977372523-15.5955042189
57.924154394611.26468581421-2.147568388963.984101842690.908788143414.26168363501-0.3607304999550.034037996964-0.8208720464630.3685137205910.0496471630543-0.05733494834130.868601864501-0.0433425875050.329100027290.4553253050870.01200696816480.04618184206340.3219084583720.04070589206520.346675579657-38.1025253809-51.228638079-0.985827701201
66.544296781550.574448582815-2.575584699265.61371314291-0.2752884350695.40640650141-0.0334303622024-0.06232211421890.0788348233264-0.01600196700850.031558602064-0.0460643027586-0.005874237314040.0697996081067-0.01259506972670.2098776654130.00475849928007-0.03084784944830.215082310457-0.007346190569350.225317212385-32.6877092246-39.7280103042-10.2601636386
74.708968349140.135909111181-4.760930222556.71936535191.191608194615.04071843771-0.08936768642870.354417849314-0.280411368921-0.996187271107-0.143013523076-0.4845294157570.08687212711080.2707573218480.1948616982280.320100285005-0.09320266082370.02160048293710.378015144330.01061276174790.264986963903-24.6592314373-35.6192534527-21.6355764497
84.957354973365.48898709496-3.884046843226.27976849361-4.098629926492.79887075707-0.3066797841570.6076483529620.492548524407-0.5327600995380.5700760123380.6052657025590.219164847776-0.473004340086-0.3131510655460.35153877637-0.0532861847648-0.07389708042150.3790123078720.0188194389560.328964738985-31.6525530168-25.500205092-25.8634299228
98.972856012432.96236809006-3.416887644194.94512308807-0.5233981076064.99255837212-0.0833770750007-0.376082613493-0.5999695695710.128701090468-0.160478810688-0.218696148030.2120504786990.09087106668860.2386724736480.3005896182190.0220265760907-0.01538910944970.1933036014630.005224104705830.194875376356-32.4249728061-45.6594888226-10.5595248222
101.414136962360.649534530347-0.164958695613.01698902794-0.4229786466692.72377796018-0.01480424832560.2007604298270.0726213572905-0.2580474288840.0138887587028-0.06476007265090.102886546386-0.0702513824963-0.002555612261580.2518810010740.03026717336250.01503825972890.3616612510350.01029696115740.219627734555-10.8580188913-7.79451739035-34.9494235774
112.388937576651.198249359260.2633176024630.6549880880021.02367365491.041309706570.02642218135540.237583524412-0.0613521834240.143639495905-0.126298144823-0.2617119549590.09048407355540.1805667023480.09618649998760.3279947480650.06510854629180.008868684712450.40678128380.07512909077380.282845682235-1.56313794833-3.79292420219-29.5502103567
123.85559902257-0.05563483370161.060318034491.85570706713-0.08787662897344.81433878518-0.01373908068740.1756363415520.09990600774130.0205949676269-0.0419482858528-0.10944167462-0.005755506430010.1154119716940.05679590941380.266429622153-0.0002494690256120.03098295512120.4789766274810.04933680867070.36213384883116.60694062665.67575330555-23.2938831004
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 131 )HA1 - 1311 - 131
22chain 'H' and (resid 132 through 187 )HA132 - 187132 - 182
33chain 'H' and (resid 188 through 225 )HA188 - 225183 - 217
44chain 'C' and (resid 335 through 364 )CB335 - 3641 - 30
55chain 'C' and (resid 365 through 393 )CB365 - 39331 - 59
66chain 'C' and (resid 394 through 442 )CB394 - 44260 - 108
77chain 'C' and (resid 443 through 459 )CB443 - 459109 - 125
88chain 'C' and (resid 460 through 494 )CB460 - 494126 - 160
99chain 'C' and (resid 495 through 527 )CB495 - 527161 - 192
1010chain 'L' and (resid 1 through 83 )LD1 - 831 - 83
1111chain 'L' and (resid 84 through 121 )LD84 - 12184 - 121
1212chain 'L' and (resid 122 through 212 )LD122 - 212122 - 212

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