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- PDB-8dcc: SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound t... -

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Basic information

Entry
Database: PDB / ID: 8dcc
TitleSARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound to P2B-2F6 Fab
Components
  • P2B-2F6 Fab heavy chain
  • P2B-2F6 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immunogen / antigen / design / vaccine / 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: 2.6 Å
AuthorsDickey, T.D. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: Sci Adv / Year: 2022
Title: Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.
Authors: Dickey, T.H. / Tang, W.K. / Butler, B. / Ouahes, T. / Orr-Gonzalez, S. / Salinas, N.D. / Lambert, L.E. / Tolia, N.H.
#1: Journal: Biorxiv / Year: 2021
Title: Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.
Authors: Dickey, T.H. / Tang, W.K. / Butler, B. / Ouahes, T. / Orr-Gonzalez, S. / Salinas, N.D. / Lambert, L.E. / Tolia, N.H.
History
DepositionJun 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
L: P2B-2F6 Fab light chain
H: P2B-2F6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1934
Polymers71,9723
Non-polymers2211
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-25 kcal/mol
Surface area28110 Å2
Unit cell
Length a, b, c (Å)71.060, 91.965, 111.149
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: Protein Spike protein S1


Mass: 23684.422 Da / Num. of mol.: 1 / Fragment: RBD SPEEDesign Immunogen 3 (UNP residues 333-526)
Mutation: T333K, A363Y, N388K, N394Y, I468T, S514T, H519D, A522P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Strain: Wuhan-Hu-1 / Gene: S, 2 / Plasmid: pHLsec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody P2B-2F6 Fab light chain


Mass: 22686.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody P2B-2F6 Fab heavy chain


Mass: 25600.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): Expi293F / 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.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M sodium fluoride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.57→70.88 Å / Num. obs: 23841 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.078 / Rrim(I) all: 0.203 / Net I/σ(I): 8.2
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.089 / Num. unique obs: 2326 / CC1/2: 0.332 / Rpim(I) all: 0.861 / Rrim(I) all: 2.262 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
autoPROC1.0.5data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7BWJ

7bwj


Resolution: 2.6→56.23 Å / SU ML: 0.4207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 1949 8.46 %
Rwork0.2205 21083 -
obs0.2247 23032 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.89 Å2
Refinement stepCycle: LAST / Resolution: 2.6→56.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 14 31 4861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074957
X-RAY DIFFRACTIONf_angle_d1.10856763
X-RAY DIFFRACTIONf_chiral_restr0.0696757
X-RAY DIFFRACTIONf_plane_restr0.0069864
X-RAY DIFFRACTIONf_dihedral_angle_d14.41091755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.42071360.35291472X-RAY DIFFRACTION99.94
2.67-2.740.38151370.32291491X-RAY DIFFRACTION99.94
2.74-2.820.35191380.30061476X-RAY DIFFRACTION99.94
2.82-2.910.32891360.29841480X-RAY DIFFRACTION99.94
2.91-3.010.35131370.29421477X-RAY DIFFRACTION100
3.01-3.130.31581370.26971493X-RAY DIFFRACTION100
3.13-3.280.32311390.26151492X-RAY DIFFRACTION100
3.28-3.450.31431370.23651488X-RAY DIFFRACTION100
3.45-3.660.29481400.23841509X-RAY DIFFRACTION100
3.66-3.950.27651380.22051502X-RAY DIFFRACTION99.94
3.95-4.340.25041390.18751504X-RAY DIFFRACTION100
4.34-4.970.2581410.17351523X-RAY DIFFRACTION99.94
4.97-6.260.22271430.19211550X-RAY DIFFRACTION100
6.26-56.230.19171510.1771626X-RAY DIFFRACTION99.55

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