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- PDB-8i5i: Crystal structure of SARS-CoV-2 delta variant spike receptor-bind... -

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Basic information

Entry
Database: PDB / ID: 8i5i
TitleCrystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab
Components
  • Fab Heavy chain
  • Fab Light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / spike / coronavirus / viral protein / Fab / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsYamamoto, A. / Higashiura, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2023
Title: Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Authors: Shitaoka, K. / Higashiura, A. / Kawano, Y. / Yamamoto, A. / Mizoguchi, Y. / Hashiguchi, T. / Nishimichi, N. / Huang, S. / Ito, A. / Ohki, S. / Kanda, M. / Taniguchi, T. / Yoshizato, R. / ...Authors: Shitaoka, K. / Higashiura, A. / Kawano, Y. / Yamamoto, A. / Mizoguchi, Y. / Hashiguchi, T. / Nishimichi, N. / Huang, S. / Ito, A. / Ohki, S. / Kanda, M. / Taniguchi, T. / Yoshizato, R. / Azuma, H. / Kitajima, Y. / Yokosaki, Y. / Okada, S. / Sakaguchi, T. / Yasuda, T.
History
DepositionJan 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Spike protein S1
H: Fab Heavy chain
L: Fab Light chain


Theoretical massNumber of molelcules
Total (without water)72,6943
Polymers72,6943
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-35 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.605, 77.605, 519.154
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Spike protein S1


Mass: 25332.432 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 / Variant: delta / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody Fab Heavy chain


Mass: 24241.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab Light chain


Mass: 23119.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.05→67.21 Å / Num. obs: 7419 / % possible obs: 88.6 % / Redundancy: 17.8 % / Biso Wilson estimate: 77.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.9
Reflection shellResolution: 3.05→3.47 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 371 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→67.21 Å / SU ML: 0.4832 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.8995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3725 386 5.21 %
Rwork0.2283 7019 -
obs0.2359 7405 39.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.16 Å2
Refinement stepCycle: LAST / Resolution: 3.06→67.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 0 0 4780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934896
X-RAY DIFFRACTIONf_angle_d1.1356654
X-RAY DIFFRACTIONf_chiral_restr0.0562736
X-RAY DIFFRACTIONf_plane_restr0.0081855
X-RAY DIFFRACTIONf_dihedral_angle_d16.84571752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.50.4292210.367393X-RAY DIFFRACTION6.84
3.5-4.410.3353860.26191463X-RAY DIFFRACTION25.15
4.41-67.210.37872790.21895163X-RAY DIFFRACTION82.24
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)
10.109354896324-0.07255827818380.08668708991750.541769727638-0.4103856955890.3183149664410.0123856736903-0.1062046175470.1882422107490.21271861257-0.02501338863830.0863655865764-0.306943086844-0.1097028031150.0100163836963-0.180900794220.156752687281-0.3461477139230.2140030444440.350876640991-0.176065771674-32.71126.90930.561
20.413988278020.00957862432359-0.2481200720550.1401558577220.0003257617277610.5488540336450.0301632032783-0.185394450249-0.1292541249280.09791139947960.2125400504560.13776229171-0.2848718503560.02046838866340.08735141432260.280579178969-0.3924926650270.02362473189430.8294911541210.1391797907360.435121746617-68.83321.0139.202
30.6900107955030.120220124022-0.1044180678960.0402340960968-0.03402675224520.210879952455-0.03141894227610.310885093478-0.1216078125080.157678147054-0.07375192824420.2253449532990.0539071580828-0.0622095998535-0.02464196248620.321132720522-0.09391539668320.02367044854360.3568848900030.1648616253960.307035565588-37.6517.82111.238
40.543224694799-0.133108546810.1662601079670.612176869129-0.2286474618122.165085854370.0619303251589-0.152302337907-0.5535583249510.198266853333-0.0499931638943-0.170424628506-0.165521534058-0.5656521048370.058458037127-0.0560597401486-0.231717453101-0.06191771929550.4369763930210.1226120928790.457612930484-65.43524.17123.226
50.2034796087280.05300591006380.04296442463440.01286726282170.01231873574240.00991899911417-0.335055188855-0.147063198359-0.9347839731420.2164099124120.2627013449160.1853677779870.153236997522-0.3544686461240.01813847783650.999627553103-0.05199226373830.4070604761950.5545757319780.04819324621550.624230191458-13.48410.635-22.581
60.120313270506-0.09205559954390.00761220635390.06805723568940.01586578317090.304195916687-0.2321212599920.2424872342340.529420017688-0.3456152902950.336723138679-0.69814243217-0.964029485786-0.355021877767-0.02243349468810.6363332714260.0102734047850.1486895166390.579897063192-0.02730166520610.559091469066-12.42622.172-31.496
70.5142190405730.02572581019450.02553802484840.268365096461-0.3333363591020.3531185879260.201250269483-0.196824554583-0.2233211780910.2273912862520.0788683252683-0.223395512445-0.154239563501-0.3306863236080.005474019663260.0779770916129-0.04722238968710.07831099016160.3360588681010.05788843987770.420192644731-15.40220.037-9.492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 1:108 )L1 - 108
2X-RAY DIFFRACTION2( CHAIN L AND RESID 109:213 )L109 - 213
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:118 )H1 - 118
4X-RAY DIFFRACTION4( CHAIN H AND RESID 119:223 )H119 - 223
5X-RAY DIFFRACTION5( CHAIN R AND RESID 335:365 )R335 - 365
6X-RAY DIFFRACTION6( CHAIN R AND RESID 366:391 )R366 - 391
7X-RAY DIFFRACTION7( CHAIN R AND RESID 392:525 )R392 - 525

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