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- PDB-7yco: Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to ... -

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Basic information

Entry
Database: PDB / ID: 7yco
TitleCrystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody
Components
  • Repebody (A6)
  • Spike protein S1
KeywordsPROTEIN BINDING / Severe acute respiratory syndrome coronavirus 2 / Complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Cyclostomatida (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsKim, U.J. / Cho, H.S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C3010506 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063903 Korea, Republic Of
CitationJournal: Antiviral Res / Year: 2023
Title: A bivalent form of a RBD-specific synthetic antibody effectively neutralizes SARS-CoV-2 variants.
Authors: Dong-Gun Kim / Uijin Kim / In Ho Park / Bumhan Ryu / Youngki Yoo / Jeong Seok Cha / Ga-Yeon Yoon / Sung-Hee Kim / Heeju Oh / Jun-Young Seo / Ki Taek Nam / Je Kyung Seong / Jeon-Soo Shin / ...Authors: Dong-Gun Kim / Uijin Kim / In Ho Park / Bumhan Ryu / Youngki Yoo / Jeong Seok Cha / Ga-Yeon Yoon / Sung-Hee Kim / Heeju Oh / Jun-Young Seo / Ki Taek Nam / Je Kyung Seong / Jeon-Soo Shin / Hyun-Soo Cho / Hak-Sung Kim /
Abstract: Coronavirus Disease 2019 (COVID-19) pandemic is severely impacting the world, and tremendous efforts have been made to deal with it. Despite many advances in vaccines and therapeutics, severe acute ...Coronavirus Disease 2019 (COVID-19) pandemic is severely impacting the world, and tremendous efforts have been made to deal with it. Despite many advances in vaccines and therapeutics, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains an intractable challenge. We present a bivalent Receptor Binding Domain (RBD)-specific synthetic antibody, specific for the RBD of wild-type (lineage A), developed from a non-antibody protein scaffold composed of LRR (Leucine-rich repeat) modules through phage display. We further reinforced the unique feature of the synthetic antibody by constructing a tandem dimeric form. The resulting bivalent form showed a broader neutralizing activity against the variants. The in vivo neutralizing efficacy of the bivalent synthetic antibody was confirmed using a human ACE2-expressing mouse model that significantly alleviated viral titer and lung infection. The present approach can be used to develop a synthetic antibody showing a broader neutralizing activity against a multitude of SARS-CoV-2 variants.
History
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Sep 9, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
B: Repebody (A6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6253
Polymers52,4042
Non-polymers2211
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint2 kcal/mol
Surface area20560 Å2
Unit cell
Length a, b, c (Å)135.966, 135.966, 69.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Spike protein S1


Mass: 22218.936 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
#2: Protein Repebody (A6)


Mass: 30184.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclostomatida (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: 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: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dihydrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→29.8 Å / Num. obs: 45636 / % possible obs: 99.93 % / Redundancy: 13.5 % / Biso Wilson estimate: 40.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08468 / Net I/σ(I): 19.88
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.972 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 4541 / CC1/2: 0.744 / CC star: 0.924 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→29.8 Å / SU ML: 0.2715 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.1058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 2734 3.06 %
Rwork0.2355 86628 -
obs0.2362 45620 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.74 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 14 119 3757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823724
X-RAY DIFFRACTIONf_angle_d1.08035066
X-RAY DIFFRACTIONf_chiral_restr0.0654571
X-RAY DIFFRACTIONf_plane_restr0.0061653
X-RAY DIFFRACTIONf_dihedral_angle_d13.51191367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.43311380.46974308X-RAY DIFFRACTION99.93
1.99-2.030.38031380.41814358X-RAY DIFFRACTION99.96
2.03-2.070.4241280.39644307X-RAY DIFFRACTION99.98
2.07-2.110.34741420.38224390X-RAY DIFFRACTION99.98
2.11-2.160.37841400.3774285X-RAY DIFFRACTION99.89
2.16-2.210.45551360.35734303X-RAY DIFFRACTION99.98
2.21-2.260.34461370.29734358X-RAY DIFFRACTION99.96
2.26-2.320.28951380.28484372X-RAY DIFFRACTION99.91
2.32-2.390.33821380.26844296X-RAY DIFFRACTION100
2.39-2.470.32241360.26364338X-RAY DIFFRACTION99.98
2.47-2.560.31241320.27234338X-RAY DIFFRACTION100
2.56-2.660.33261330.27124315X-RAY DIFFRACTION100
2.66-2.780.28941420.26164345X-RAY DIFFRACTION99.96
2.78-2.930.32291360.28654329X-RAY DIFFRACTION99.96
2.93-3.110.3171340.26744324X-RAY DIFFRACTION100
3.11-3.350.25361440.24144317X-RAY DIFFRACTION99.96
3.35-3.690.22481360.21374348X-RAY DIFFRACTION100
3.69-4.220.20921360.19444320X-RAY DIFFRACTION100
4.22-5.310.20161360.16814340X-RAY DIFFRACTION100
5.31-29.80.19521340.18114337X-RAY DIFFRACTION100

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