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- PDB-7fbk: Crystal structure of SARS-CoV-2 receptor binding domain N501Y mut... -

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Basic information

Entry
Database: PDB / ID: 7fbk
TitleCrystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6
Components
  • New antigen receptor variable domain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Spike glycoprotein / RBD / VNAR / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Chiloscyllium plagiosum (whitespotted bambooshark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhu, J. / Xu, T. / Feng, B. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Small Methods / Year: 2022
Title: A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape.
Authors: Feng, B. / Chen, Z. / Sun, J. / Xu, T. / Wang, Q. / Yi, H. / Niu, X. / Zhu, J. / Fan, M. / Hou, R. / Shao, Y. / Huang, S. / Li, C. / Hu, P. / Zheng, P. / He, P. / Luo, J. / Yan, Q. / Xiong, ...Authors: Feng, B. / Chen, Z. / Sun, J. / Xu, T. / Wang, Q. / Yi, H. / Niu, X. / Zhu, J. / Fan, M. / Hou, R. / Shao, Y. / Huang, S. / Li, C. / Hu, P. / Zheng, P. / He, P. / Luo, J. / Yan, Q. / Xiong, X. / Liu, J. / Zhao, J. / Chen, L.
History
DepositionJul 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: New antigen receptor variable domain
D: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2686
Polymers80,1274
Non-polymers1,1412
Water2,954164
1
A: Spike protein S1
C: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6343
Polymers40,0632
Non-polymers5711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
D: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6343
Polymers40,0632
Non-polymers5711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.510, 90.531, 162.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Spike protein S1


Mass: 25672.592 Da / Num. of mol.: 2 / Fragment: receptor binding domain / Mutation: N501Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Plasmid: pSECtag2A / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Protein New antigen receptor variable domain


Mass: 14390.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chiloscyllium plagiosum (whitespotted bambooshark)
Production host: Escherichia coli (E. coli)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0.19 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 70mM Citric acid, 30mM Bis-Tris propane pH 3.4, 20% PEG 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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→19.82 Å / Num. obs: 63067 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 16.5 / Num. measured all: 786807 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.948.70.9833621541750.8490.3511.046299.7
8.91-19.8210.70.04867826340.9990.0140.0541.490.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FBJ

7fbj


Resolution: 1.9→19.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.745 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 3030 4.8 %RANDOM
Rwork0.1969 ---
obs0.1989 59970 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.39 Å2 / Biso mean: 50.554 Å2 / Biso min: 30.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å2-0 Å2-0 Å2
2---4.86 Å20 Å2
3---3.55 Å2
Refinement stepCycle: final / Resolution: 1.9→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 76 164 5106
Biso mean--83.1 47.87 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135102
X-RAY DIFFRACTIONr_bond_other_d0.0010.0144558
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.6786946
X-RAY DIFFRACTIONr_angle_other_deg1.3891.60110500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9875620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99721.957276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32115778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5181533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 215 -
Rwork0.338 4375 -
all-4590 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7337-0.47810.71190.7435-0.05792.0997-0.02250.1052-0.2166-0.1213-0.0011-0.073-0.053-0.17990.02360.0629-0.01850.02730.2851-0.01050.240921.38158.11718.717
20.8426-0.59540.53081.6675-0.47171.0015-0.00410.05020.0018-0.07160.07230.23760.04830.1059-0.06820.0114-0.01530.01520.23440.00040.39597.83424.1933.169
30.91750.2187-0.74452.9129-0.26692.24860.06010.10020.1293-0.01130.0546-0.0037-0.50610.0171-0.11470.34640.04770.03450.27490.0710.103620.25881.8468.97
40.3166-0.19710.07291.44680.67942.59-0.2031-0.0231-0.03970.0991-0.04550.04-0.0733-0.01970.24860.12550.02010.02580.23760.0310.48745.11847.37544.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A334 - 529
2X-RAY DIFFRACTION2B334 - 529
3X-RAY DIFFRACTION3C0 - 112
4X-RAY DIFFRACTION4D0 - 112

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