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- PDB-7vyr: Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27... -

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Basic information

Entry
Database: PDB / ID: 7vyr
TitleCrystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment
Components
  • D27 heavy chain
  • D27 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Computational design / Neutralizing antibody / SARS-CoV-2 / VIRAL PROTEIN / IMMUNE SYSTEM / 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 / symbiont-mediated suppression of host innate immune response / 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 / 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: 2.2 Å
AuthorsJeong, B.-S. / Oh, B.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentMCM-2021-N11210036 Korea, Republic Of
CitationJournal: Mabs / Year: 2022
Title: Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants.
Authors: Jeong, B.S. / Cha, J.S. / Hwang, I. / Kim, U. / Adolf-Bryfogle, J. / Coventry, B. / Cho, H.S. / Kim, K.D. / Oh, B.H.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: D27 heavy chain
L: D27 light chain
R: Spike protein S1
A: D27 heavy chain
B: D27 light chain
C: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)164,8516
Polymers164,8516
Non-polymers00
Water8,287460
1
H: D27 heavy chain
L: D27 light chain
R: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)82,4253
Polymers82,4253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: D27 heavy chain
B: D27 light chain
C: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)82,4253
Polymers82,4253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.801, 191.676, 65.900
Angle α, β, γ (deg.)90.000, 93.988, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody D27 heavy chain


Mass: 27037.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody D27 light chain


Mass: 26123.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Spike protein S1


Mass: 29265.166 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% (v/v) PEG 3350, 200mM NH4Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.92 Å / Num. obs: 74394 / % possible obs: 95.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.47 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 1.36
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.2674 / Num. unique obs: 6968 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MIK, 7JMO

4mik

7jmo


Resolution: 2.2→47.92 Å / SU ML: 0.2451 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.3503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 1296 1.76 %
Rwork0.192 72373 -
obs0.1928 73669 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 0 0 460 9940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00879708
X-RAY DIFFRACTIONf_angle_d1.215513204
X-RAY DIFFRACTIONf_chiral_restr0.06851448
X-RAY DIFFRACTIONf_plane_restr0.0081718
X-RAY DIFFRACTIONf_dihedral_angle_d14.13211342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.28591410.22047617X-RAY DIFFRACTION90.44
2.29-2.390.30231310.21967685X-RAY DIFFRACTION91.63
2.39-2.520.28111440.21687825X-RAY DIFFRACTION93.19
2.52-2.680.27841410.21788026X-RAY DIFFRACTION95.06
2.68-2.880.27131380.21487917X-RAY DIFFRACTION94.09
2.88-3.170.24521470.2168329X-RAY DIFFRACTION98.93
3.17-3.630.23221600.19228380X-RAY DIFFRACTION99.08
3.63-4.570.20231440.15978216X-RAY DIFFRACTION97.54
4.58-47.920.18421500.16518378X-RAY DIFFRACTION98.42

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