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- PDB-7cyv: Crystal structure of FD20, a neutralizing single-chain variable f... -

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Basic information

Entry
Database: PDB / ID: 7cyv
TitleCrystal structure of FD20, a neutralizing single-chain variable fragment (scFv) in complex with SARS-CoV-2 Spike receptor-binding domain (RBD)
Components
  • Spike protein S1
  • The heavy chain variable region of the scFv FD20,The light chain variable region of the scFv FD20
KeywordsVIRAL PROTEIN / coronavirus / Covid-19 / nCoV-2019 / neutralizing antibody / receptor-binding domain / SARS-CoV-2 / scFv / single-chain variable fragment / Spike
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 / viral translation / 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 / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / 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: 3.13 Å
AuthorsLi, Y. / Li, T. / Lai, Y. / Cai, H. / Yao, H. / Li, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870726 China
CitationJournal: Embo Mol Med / Year: 2021
Title: Uncovering a conserved vulnerability site in SARS-CoV-2 by a human antibody.
Authors: Li, T. / Cai, H. / Zhao, Y. / Li, Y. / Lai, Y. / Yao, H. / Liu, L.D. / Sun, Z. / van Vlissingen, M.F. / Kuiken, T. / GeurtsvanKessel, C.H. / Zhang, N. / Zhou, B. / Lu, L. / Gong, Y. / Qin, W. ...Authors: Li, T. / Cai, H. / Zhao, Y. / Li, Y. / Lai, Y. / Yao, H. / Liu, L.D. / Sun, Z. / van Vlissingen, M.F. / Kuiken, T. / GeurtsvanKessel, C.H. / Zhang, N. / Zhou, B. / Lu, L. / Gong, Y. / Qin, W. / Mondal, M. / Duan, B. / Xu, S. / Richard, A.S. / Raoul, H. / Chen, J. / Xu, C. / Wu, L. / Zhou, H. / Huang, Z. / Zhang, X. / Li, J. / Wang, Y. / Bi, Y. / Rockx, B. / Chen, J. / Meng, F.L. / Lavillette, D. / Li, D.
History
DepositionSep 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: 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: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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

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Assembly

Deposited unit
H: The heavy chain variable region of the scFv FD20,The light chain variable region of the scFv FD20
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3203
Polymers53,4412
Non-polymers8791
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint22 kcal/mol
Surface area20130 Å2
Unit cell
Length a, b, c (Å)206.958, 57.925, 47.207
Angle α, β, γ (deg.)90.000, 100.433, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody The heavy chain variable region of the scFv FD20,The light chain variable region of the scFv FD20


Mass: 29613.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of tag (GSSS), heavy chain variable region of the scFv FD20 (residues 0-125), linker (GGGSGGGGSGGGGSS), light chain variable region of the scFv FD20 (residues 1002-1129), and tag (HHHHHH)
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 23827.623 Da / Num. of mol.: 1 / Fragment: receptor-binding domain (RBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.13→46.43 Å / Num. obs: 9847 / % possible obs: 98.89 % / Redundancy: 5.2 % / Biso Wilson estimate: 65.25 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.2724 / Rpim(I) all: 0.1322 / Net I/σ(I): 5.65
Reflection shellResolution: 3.13→3.24 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 927 / CC1/2: 0.791 / Rpim(I) all: 0.5387 / % possible all: 94.68

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MOJ, 5C6W

6moj

5c6w


Resolution: 3.13→46.43 Å / SU ML: 0.5228 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2762 461 4.72 %
Rwork0.2518 9303 -
obs0.2529 9764 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.91 Å2
Refinement stepCycle: LAST / Resolution: 3.13→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 59 0 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413306
X-RAY DIFFRACTIONf_angle_d0.79444524
X-RAY DIFFRACTIONf_chiral_restr0.0525517
X-RAY DIFFRACTIONf_plane_restr0.0044578
X-RAY DIFFRACTIONf_dihedral_angle_d17.7798515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.240.38951380.3393055X-RAY DIFFRACTION98.1
3.58-4.510.27891730.24913066X-RAY DIFFRACTION99.39
4.52-46.430.22591500.21723182X-RAY DIFFRACTION99.26

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