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- PDB-7dk0: Crystal structure of SARS-CoV-2 Spike RBD in complex with MW05 Fab -

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Basic information

Entry
Database: PDB / ID: 7dk0
TitleCrystal structure of SARS-CoV-2 Spike RBD in complex with MW05 Fab
Components
  • MW05 heavy chain
  • MW05 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / Spike / RBD / Antibody / ADE / 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 / molecular replacement / Resolution: 3.199 Å
AuthorsWang, J. / Jiao, S. / Wang, R. / Zhang, J. / Zhang, M. / Wang, M.
CitationJournal: Commun Biol / Year: 2022
Title: Antibody-dependent enhancement (ADE) of SARS-CoV-2 pseudoviral infection requires Fc gamma RIIB and virus-antibody complex with bivalent interaction.
Authors: Wang, S. / Wang, J. / Yu, X. / Jiang, W. / Chen, S. / Wang, R. / Wang, M. / Jiao, S. / Yang, Y. / Wang, W. / Chen, H. / Chen, B. / Gu, C. / Liu, C. / Wang, A. / Wang, M. / Li, G. / Guo, C. / ...Authors: Wang, S. / Wang, J. / Yu, X. / Jiang, W. / Chen, S. / Wang, R. / Wang, M. / Jiao, S. / Yang, Y. / Wang, W. / Chen, H. / Chen, B. / Gu, C. / Liu, C. / Wang, A. / Wang, M. / Li, G. / Guo, C. / Liu, D. / Zhang, J. / Zhang, M. / Wang, L. / Gui, X.
History
DepositionNov 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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
A: MW05 heavy chain
B: MW05 light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1574
Polymers71,9353
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.000, 87.000, 216.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody MW05 heavy chain


Mass: 23855.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody MW05 light chain


Mass: 22957.510 Da / Num. of mol.: 1
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 / S glycoprotein / E2 / Peplomer protein


Mass: 25122.336 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY

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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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic, 21% (w/v) PEG 3350, 0.02 M urea

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.199→50 Å / Num. obs: 16375 / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.028 / Rrim(I) all: 0.121 / Χ2: 0.966 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3119.91.70915680.7730.391.7530.891100
3.31-3.4519.21.05416140.8960.2451.0820.903100
3.45-3.618.40.61916150.9480.1470.6360.916100
3.6-3.7920.40.4416110.9780.0990.4510.922100
3.79-4.0320.10.24115940.9940.0550.2470.954100
4.03-4.3419.70.13716430.9970.0310.140.943100
4.34-4.78180.08716250.9980.0210.0890.96100
4.78-5.4719.80.07716500.9990.0180.0791.004100
5.47-6.8917.90.07116700.9990.0170.0741.032100
6.89-5016.20.05517850.9990.0140.0561.15499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG, 6JJP

6lzg

6jjp


Resolution: 3.199→36.083 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 832 5.12 %
Rwork0.2183 15409 -
obs0.2207 16241 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.69 Å2 / Biso mean: 92.3691 Å2 / Biso min: 59.3 Å2
Refinement stepCycle: final / Resolution: 3.199→36.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 14 0 4786
Biso mean--105.9 --
Num. residues----627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1994-3.39970.3651420.31612482100
3.3997-3.66190.3521370.29162551100
3.6619-4.030.31511200.26292540100
4.03-4.61210.25021250.20742588100
4.6121-5.80690.25511660.19622582100
5.8069-36.0830.21981420.1855266698

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