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- PDB-9fc2: The crystal structure of the SARS-CoV-2 receptor binding domain i... -

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Basic information

Entry
Database: PDB / ID: 9fc2
TitleThe crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.
Components
  • Nanobody 4
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / coronavirus / COVID-19 / RBD / SARS-CoV-2 / spike / nanobodies / neutralization / VIRAL PROTEIN
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 / 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 ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / 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 / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
ACETATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsCasasnovas, J.M. / Fernandez, L.A. / Silva, K.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)202020E079 Spain
Citation
Journal: Mabs / Year: 2025
Title: Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants.
Authors: Cerdan, L. / Silva, K. / Rodriguez-Martin, D. / Perez, P. / Noriega, M.A. / Esteban Martin, A. / Gutierrez-Adan, A. / Margolles, Y. / Corbera, J.A. / Martin-Acebes, M.A. / Garcia-Arriaza, J. ...Authors: Cerdan, L. / Silva, K. / Rodriguez-Martin, D. / Perez, P. / Noriega, M.A. / Esteban Martin, A. / Gutierrez-Adan, A. / Margolles, Y. / Corbera, J.A. / Martin-Acebes, M.A. / Garcia-Arriaza, J. / Fernandez-Recio, J. / Fernandez, L.A. / Casasnovas, J.M.
#1: Journal: Front Immunol / Year: 2022
Title: Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron.
Authors: José M Casasnovas / Yago Margolles / María A Noriega / María Guzmán / Rocío Arranz / Roberto Melero / Mercedes Casanova / Juan Alberto Corbera / Nereida Jiménez-de-Oya / Pablo ...Authors: José M Casasnovas / Yago Margolles / María A Noriega / María Guzmán / Rocío Arranz / Roberto Melero / Mercedes Casanova / Juan Alberto Corbera / Nereida Jiménez-de-Oya / Pablo Gastaminza / Urtzi Garaigorta / Juan Carlos Saiz / Miguel Ángel Martín-Acebes / Luis Ángel Fernández /
Abstract: The emergence of SARS-CoV-2 variants that escape from immune neutralization are challenging vaccines and antibodies developed to stop the COVID-19 pandemic. Thus, it is important to establish ...The emergence of SARS-CoV-2 variants that escape from immune neutralization are challenging vaccines and antibodies developed to stop the COVID-19 pandemic. Thus, it is important to establish therapeutics directed toward multiple or specific SARS-CoV-2 variants. The envelope spike (S) glycoprotein of SARS-CoV-2 is the key target of neutralizing antibodies (Abs). We selected a panel of nine nanobodies (Nbs) from dromedary camels immunized with the receptor-binding domain (RBD) of the S, and engineered Nb fusions as humanized heavy chain Abs (hcAbs). Nbs and derived hcAbs bound with subnanomolar or picomolar affinities to the S and its RBD, and S-binding cross-competition clustered them in two different groups. Most of the hcAbs hindered RBD binding to its human ACE2 (hACE2) receptor, blocked cell entry of viruses pseudotyped with the S protein and neutralized SARS-CoV-2 infection in cell cultures. Four potent neutralizing hcAbs prevented the progression to lethal SARS-CoV-2 infection in hACE2-transgenic mice, demonstrating their therapeutic potential. Cryo-electron microscopy identified Nb binding epitopes in and out the receptor binding motif (RBM), and showed different ways to prevent virus binding to its cell entry receptor. The Nb binding modes were consistent with its recognition of SARS-CoV-2 RBD variants; mono and bispecific hcAbs efficiently bound all variants of concern except omicron, which emphasized the immune escape capacity of this latest variant.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: Nanobody 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9006
Polymers36,4962
Non-polymers4044
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint1 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.664, 97.664, 64.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein / Antibody / Sugars , 3 types, 3 molecules AB

#1: Protein Spike protein S1


Mass: 23158.027 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 / Plasmid: pBJ5-GS / Cell (production host): Epithelial / Cell line (production host): CHO Lec. 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): Ovary / References: UniProt: P0DTC2
#2: Antibody Nanobody 4


Mass: 13337.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: Flag-MCS-pcDNA3.1 / Cell (production host): epithelial / Cell line (production host): HEK293F / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): Embryo
#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
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

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Non-polymers , 3 types, 367 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.5 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 22,5 % PEG 8000, 100mM NaAc pH 4.5, 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.21→48.832 Å / Num. obs: 103166 / % possible obs: 97.22 % / Redundancy: 9.89 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 0.9996 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Net I/σ(I): 22.245
Reflection shellResolution: 1.21→1.231 Å / Redundancy: 8.33 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.212 / Num. unique obs: 5301 / CC1/2: 0.8234 / Rpim(I) all: 0.3 / Rrim(I) all: 0.868 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→42.29 Å / SU ML: 0.1225 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1696 5193 5.03 %
Rwork0.1525 97971 -
obs0.1534 103164 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.71 Å2
Refinement stepCycle: LAST / Resolution: 1.21→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 26 364 2829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152679
X-RAY DIFFRACTIONf_angle_d1.21593670
X-RAY DIFFRACTIONf_chiral_restr0.1015397
X-RAY DIFFRACTIONf_plane_restr0.0129486
X-RAY DIFFRACTIONf_dihedral_angle_d6.9675403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.25171810.21673336X-RAY DIFFRACTION100
1.22-1.240.2911770.21093367X-RAY DIFFRACTION100
1.24-1.250.25711570.20672913X-RAY DIFFRACTION95.76
1.26-1.270.2604690.1871951X-RAY DIFFRACTION100
1.27-1.290.211660.1783369X-RAY DIFFRACTION100
1.29-1.30.18311800.16343322X-RAY DIFFRACTION100
1.3-1.320.20551450.15723375X-RAY DIFFRACTION100
1.32-1.340.18982110.14673325X-RAY DIFFRACTION100
1.34-1.360.17821770.15393333X-RAY DIFFRACTION100
1.36-1.390.21141500.15243337X-RAY DIFFRACTION100
1.39-1.410.19361780.14363391X-RAY DIFFRACTION100
1.41-1.440.17661820.14763348X-RAY DIFFRACTION100
1.44-1.460.17131730.14653367X-RAY DIFFRACTION100
1.46-1.490.1831840.14113330X-RAY DIFFRACTION100
1.49-1.530.16631710.14733349X-RAY DIFFRACTION100
1.53-1.560.15521850.1383349X-RAY DIFFRACTION100
1.56-1.60.17511930.13213343X-RAY DIFFRACTION100
1.6-1.640.1681860.13573342X-RAY DIFFRACTION100
1.64-1.690.17461950.13683340X-RAY DIFFRACTION100
1.69-1.750.17061810.14123372X-RAY DIFFRACTION100
1.75-1.810.17391660.14223355X-RAY DIFFRACTION100
1.81-1.880.17511860.14613353X-RAY DIFFRACTION100
1.88-1.970.17191700.14863354X-RAY DIFFRACTION100
1.97-2.070.15671880.13913360X-RAY DIFFRACTION100
2.07-2.20.16271790.14723362X-RAY DIFFRACTION100
2.2-2.370.15641590.15453401X-RAY DIFFRACTION100
2.37-2.610.17331650.16293391X-RAY DIFFRACTION100
2.61-2.980.17931760.16183382X-RAY DIFFRACTION100
2.98-3.760.16231870.15893404X-RAY DIFFRACTION100
3.76-42.290.15261760.14953450X-RAY DIFFRACTION100

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