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- PDB-7yow: Crystal structure of SARS-CoV-2 omicron variant spike receptor-bi... -

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Basic information

Entry
Database: PDB / ID: 7yow
TitleCrystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab
Components
  • Fab Heavy chain
  • Fab Light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / spike / coronavirus omicron strain / viral protein / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRUS / IMMUNE SYSTEM-VIRAL PROTEIN 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 / 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: 3.3 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
DepositionAug 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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
L: Fab Light chain
H: Fab Heavy chain
R: Spike protein S1
A: Fab Light chain
B: Fab Heavy chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,03718
Polymers146,8856
Non-polymers1,15312
Water00
1
L: Fab Light chain
H: Fab Heavy chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,11510
Polymers73,4423
Non-polymers6727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-105 kcal/mol
Surface area27580 Å2
MethodPISA
2
A: Fab Light chain
B: Fab Heavy chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9238
Polymers73,4423
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-100 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.550, 115.682, 99.487
Angle α, β, γ (deg.)90.00, 105.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain R and (resid 334 through 359 or resid 376 through 529))
211(chain C and (resid 334 through 359 or resid 376 through 517 or resid 520 through 529))
112chain H
212(chain B and (resid 2 through 132 or resid 138 through 217))
113chain L
213chain A

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Fab Light chain


Mass: 23276.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab Heavy chain


Mass: 24611.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 25553.861 Da / Num. of mol.: 2
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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
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: 3.52 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5 M ammonium sulfate, 19.5% PEG 3350, 1 mM EDTA, 10% golycerol, 0.1 M Bis-Tris pH 5.5

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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: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→49.5 Å / Num. obs: 30152 / % possible obs: 97.8 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Net I/σ(I): 5.5
Reflection shellResolution: 3.4→3.48 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4430 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WNB

7wnb


Resolution: 3.3→47.843 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1482 4.92 %
Rwork0.2085 --
obs0.2108 30099 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→47.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9590 0 60 0 9650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089888
X-RAY DIFFRACTIONf_angle_d1.01313466
X-RAY DIFFRACTIONf_dihedral_angle_d12.1225866
X-RAY DIFFRACTIONf_chiral_restr0.0511485
X-RAY DIFFRACTIONf_plane_restr0.0071721
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11R1429X-RAY DIFFRACTIONPOSITIONAL
12C1429X-RAY DIFFRACTIONPOSITIONAL0.051
21H1581X-RAY DIFFRACTIONPOSITIONAL
22B1581X-RAY DIFFRACTIONPOSITIONAL0.057
31L1636X-RAY DIFFRACTIONPOSITIONAL
32A1636X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.40670.40831400.32862624X-RAY DIFFRACTION99
3.4067-3.52840.31171410.28342597X-RAY DIFFRACTION98
3.5284-3.66960.3451210.24542609X-RAY DIFFRACTION98
3.6696-3.83660.27281290.24532629X-RAY DIFFRACTION98
3.8366-4.03880.27971220.23262586X-RAY DIFFRACTION97
4.0388-4.29170.25511250.22462584X-RAY DIFFRACTION97
4.2917-4.62280.25341480.18322557X-RAY DIFFRACTION97
4.6228-5.08750.23311340.18252547X-RAY DIFFRACTION96
5.0875-5.82260.25751300.1832632X-RAY DIFFRACTION97
5.8226-7.33160.22191520.21072585X-RAY DIFFRACTION98
7.3316-47.8430.22141400.18422667X-RAY DIFFRACTION98

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