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- PDB-7deo: Crystal structure of SARS-CoV-2 RBD in complex with a neutralizin... -

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Basic information

Entry
Database: PDB / ID: 7deo
TitleCrystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv
Components
  • Spike protein S1
  • antibody scFv
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / SARS-CoV-2 / RBD / antibody / VIRAL PROTEIN / ANTIVIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN 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 / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / 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 / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFu, D. / Zhang, G. / Li, X. / Rao, Z. / Guo, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670731 China
National Natural Science Foundation of China (NSFC)31870733 China
CitationJournal: Plos Biol. / Year: 2021
Title: Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.
Authors: Fu, D. / Zhang, G. / Wang, Y. / Zhang, Z. / Hu, H. / Shen, S. / Wu, J. / Li, B. / Li, X. / Fang, Y. / Liu, J. / Wang, Q. / Zhou, Y. / Wang, W. / Li, Y. / Lu, Z. / Wang, X. / Nie, C. / Tian, ...Authors: Fu, D. / Zhang, G. / Wang, Y. / Zhang, Z. / Hu, H. / Shen, S. / Wu, J. / Li, B. / Li, X. / Fang, Y. / Liu, J. / Wang, Q. / Zhou, Y. / Wang, W. / Li, Y. / Lu, Z. / Wang, X. / Nie, C. / Tian, Y. / Chen, D. / Wang, Y. / Zhou, X. / Wang, Q. / Yu, F. / Zhang, C. / Deng, C. / Zhou, L. / Guan, G. / Shao, N. / Lou, Z. / Deng, F. / Zhang, H. / Chen, X. / Wang, M. / Liu, L. / Rao, Z. / Guo, Y.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: 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
Revision 1.2Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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
A: antibody scFv
B: Spike protein S1
C: antibody scFv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1528
Polymers101,6294
Non-polymers5234
Water5,855325
1
A: antibody scFv
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0764
Polymers50,8152
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-13 kcal/mol
Surface area20090 Å2
MethodPISA
2
C: antibody scFv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0764
Polymers50,8152
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-14 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.080, 160.609, 42.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody antibody scFv


Mass: 27654.650 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: Protein Spike protein S1


Mass: 23159.947 Da / Num. of mol.: 2 / Fragment: RBD
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#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.: 2 / 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.: 325 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1% w/v Tryptone, 0.001M Sodium azide, 0.05M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 70511 / % possible obs: 99.4 % / Redundancy: 4.4 % / CC1/2: 0.979 / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.525 / Num. unique obs: 4161 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJF

7cjf


Resolution: 2.5→49.49 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 3694 5.33 %
Rwork0.1872 65661 -
obs0.1896 69355 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.96 Å2 / Biso mean: 32.439 Å2 / Biso min: 12.37 Å2
Refinement stepCycle: final / Resolution: 2.5→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6769 0 30 325 7124
Biso mean--56.89 32.1 -
Num. residues----871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.530.35641290.29492410253995
2.53-2.570.38061340.29722500263497
2.57-2.60.32441530.28532554270798
2.6-2.640.29961360.27862584272098
2.64-2.680.35221540.27322480263498
2.68-2.730.33511290.27182543267299
2.73-2.780.30751440.25682597274199
2.78-2.830.34451510.24092566271798
2.83-2.880.27071460.2312496264299
2.88-2.940.29461300.22972523265398
2.94-30.29261580.22752598275698
3-3.070.24611310.21822505263698
3.07-3.150.2371480.21772514266299
3.15-3.230.22241580.19012602276099
3.23-3.330.25341340.19712496263099
3.33-3.440.23341490.1792534268398
3.44-3.560.20421320.18042537266996
3.56-3.70.25781320.1812364249693
3.7-3.870.22041410.17272604274599
3.87-4.080.22861510.156925192670100
4.08-4.330.16151350.12742579271499
4.33-4.660.14781450.12562583272899
4.66-5.130.16541510.12552514266598
5.13-5.880.18591400.14262517265797
5.88-7.40.16511440.16942438258295
7.4-49.490.20221390.16262504264396

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