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- PDB-7cm4: Crystal Structure of COVID-19 virus spike receptor-binding domain... -

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Basic information

Entry
Database: PDB / ID: 7cm4
TitleCrystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59
Components
  • IgG heavy chain
  • IgG light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-Cov-2 / spike / receptor binding domain / RBD / IgG / Fab
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 / 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 / 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
NICKEL (II) ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsKim, Y.G. / Jeong, J.H. / Bae, J.S. / Lee, J.
CitationJournal: Nat Commun / Year: 2021
Title: A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein.
Authors: Kim, C. / Ryu, D.K. / Lee, J. / Kim, Y.I. / Seo, J.M. / Kim, Y.G. / Jeong, J.H. / Kim, M. / Kim, J.I. / Kim, P. / Bae, J.S. / Shim, E.Y. / Lee, M.S. / Kim, M.S. / Noh, H. / Park, G.S. / ...Authors: Kim, C. / Ryu, D.K. / Lee, J. / Kim, Y.I. / Seo, J.M. / Kim, Y.G. / Jeong, J.H. / Kim, M. / Kim, J.I. / Kim, P. / Bae, J.S. / Shim, E.Y. / Lee, M.S. / Kim, M.S. / Noh, H. / Park, G.S. / Park, J.S. / Son, D. / An, Y. / Lee, J.N. / Kwon, K.S. / Lee, J.Y. / Lee, H. / Yang, J.S. / Kim, K.C. / Kim, S.S. / Woo, H.M. / Kim, J.W. / Park, M.S. / Yu, K.M. / Kim, S.M. / Kim, E.H. / Park, S.J. / Jeong, S.T. / Yu, C.H. / Song, Y. / Gu, S.H. / Oh, H. / Koo, B.S. / Hong, J.J. / Ryu, C.M. / Park, W.B. / Oh, M.D. / Choi, Y.K. / Lee, S.Y.
History
DepositionJul 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein
H: IgG heavy chain
L: IgG light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9738
Polymers98,8373
Non-polymers1,1365
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-24 kcal/mol
Surface area29500 Å2
Unit cell
Length a, b, c (Å)65.550, 167.600, 169.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody IgG heavy chain


Mass: 50547.078 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: Antibody IgG light chain


Mass: 22655.049 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)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 25634.781 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 69 molecules

#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-Cl pH 8.0 16% (w/v) Polyethylene glycol monomethyl ether 2,000 10 mM Nickel(II) Chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 7, 2020
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.71→29.76 Å / Num. obs: 25744 / % possible obs: 99.78 % / Redundancy: 13.6 % / Biso Wilson estimate: 58.06 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.06856 / Rrim(I) all: 0.2543 / Net I/σ(I): 12.44
Reflection shellResolution: 2.71→2.807 Å / Redundancy: 99.88 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2541 / CC1/2: 0.606 / CC star: 0.869 / Rpim(I) all: 0.6129 / Rrim(I) all: 2.232

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Processing

Software
NameVersionClassification
Coot0.8.9.1refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.71→29.76 Å / SU ML: 0.3896 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 2006 7.79 %
Rwork0.2166 23729 -
obs0.2186 25735 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.14 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 70 65 4985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255041
X-RAY DIFFRACTIONf_angle_d0.5886876
X-RAY DIFFRACTIONf_chiral_restr0.0437788
X-RAY DIFFRACTIONf_plane_restr0.0047871
X-RAY DIFFRACTIONf_dihedral_angle_d13.64611811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.39411430.30871650X-RAY DIFFRACTION99.89
2.78-2.850.34521430.30021683X-RAY DIFFRACTION99.89
2.85-2.940.3611390.29861676X-RAY DIFFRACTION100
2.94-3.030.30581400.27611660X-RAY DIFFRACTION99.89
3.03-3.140.30751410.27071676X-RAY DIFFRACTION99.94
3.14-3.270.22961470.2471678X-RAY DIFFRACTION99.95
3.27-3.410.29051430.25211676X-RAY DIFFRACTION99.95
3.41-3.590.3041410.24061689X-RAY DIFFRACTION99.89
3.59-3.820.2561390.21291690X-RAY DIFFRACTION99.95
3.82-4.110.20961420.20491713X-RAY DIFFRACTION100
4.11-4.520.16971460.17141680X-RAY DIFFRACTION99.89
4.52-5.180.19161450.1651718X-RAY DIFFRACTION99.79
5.18-6.510.20811470.19691737X-RAY DIFFRACTION99.95
6.51-29.760.23611500.20671803X-RAY DIFFRACTION99.59

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