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- PDB-7s4s: Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) i... -

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Basic information

Entry
Database: PDB / ID: 7s4s
TitleCrystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab
Components
  • CoV11 heavy chain
  • CoV11 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/Immune System / SARS-CoV-2 S RBD Fab complex / SARS-CoV-2 S receptor-binding domain antibody Fab complex / COVID-19 spike protein antibody Fab 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 / 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
ACETATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Front Immunol / Year: 2023
Title: The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Authors: Tolbert, W.D. / Chen, Y. / Sun, L. / Benlarbi, M. / Ding, S. / Manickam, R. / Pangaro, E. / Nguyen, D.N. / Gottumukkala, S. / Cote, M. / Gonzalez, F.J. / Finzi, A. / Tehrani, Z.R. / Sajadi, M.M. / Pazgier, M.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: CoV11 heavy chain
L: CoV11 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,93113
Polymers72,9943
Non-polymers93810
Water10,215567
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.056, 111.259, 142.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody CoV11 heavy chain


Mass: 23362.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody CoV11 light chain


Mass: 23536.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike protein S1


Mass: 26095.348 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 / Cell (production host): HEK293 GnT1- cells / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#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: isolated from a genetically manipulated source
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

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Non-polymers , 3 types, 576 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 4000 150 mM ammonium sulfate 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 54854 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 0.978 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.073 / Net I/σ(I): 11.6
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 2504 / CC1/2: 0.567 / Rpim(I) all: 0.425 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMP

7jmp


Resolution: 2.05→35.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 2710 5.07 %
Rwork0.1657 --
obs0.1673 53446 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 55 567 5429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085025
X-RAY DIFFRACTIONf_angle_d0.986842
X-RAY DIFFRACTIONf_dihedral_angle_d20.147707
X-RAY DIFFRACTIONf_chiral_restr0.062750
X-RAY DIFFRACTIONf_plane_restr0.005888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.2758900.23011856X-RAY DIFFRACTION67
2.08-2.120.25071190.21472397X-RAY DIFFRACTION85
2.12-2.170.24341270.20472494X-RAY DIFFRACTION90
2.17-2.220.25261330.20472633X-RAY DIFFRACTION95
2.22-2.270.23381640.19682644X-RAY DIFFRACTION97
2.27-2.320.25011480.19042704X-RAY DIFFRACTION98
2.32-2.390.21641430.18832744X-RAY DIFFRACTION98
2.39-2.460.23671400.19212655X-RAY DIFFRACTION97
2.46-2.540.24581340.18982673X-RAY DIFFRACTION96
2.54-2.630.22821470.18012796X-RAY DIFFRACTION99
2.63-2.730.21921680.17242738X-RAY DIFFRACTION99
2.73-2.860.20761350.18132779X-RAY DIFFRACTION99
2.86-3.010.22581480.17192780X-RAY DIFFRACTION99
3.01-3.190.22381270.16922764X-RAY DIFFRACTION98
3.19-3.440.1931460.16482752X-RAY DIFFRACTION97
3.44-3.790.19041580.15182805X-RAY DIFFRACTION100
3.79-4.330.15211430.13212835X-RAY DIFFRACTION99
4.33-5.460.15041660.12292781X-RAY DIFFRACTION97
5.46-35.90.17421740.16952906X-RAY DIFFRACTION97
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)
12.58950.4496-0.48272.75930.19243.43780.1013-0.3872-0.01630.513-0.16440.21850.0872-0.2850.04940.2666-0.02010.03390.2074-0.02340.20814.3391-16.4529-13.5826
21.0163-0.3064-0.90270.26570.37240.99720.0053-0.07220.1434-0.04050.0599-0.0267-0.04130.0968-0.08750.2007-0.02-0.02820.21270.00230.251538.9608-27.8192-42.6055
31.8221-0.8636-1.04130.84120.53960.96370.00890.08590.0268-0.0056-0.0397-0.01480.0399-0.05960.04060.1403-0.021-0.02540.12590.01510.14628.7003-38.581-53.6045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 334 through 1001)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 214)
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 214)

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