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- PDB-8h5t: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -

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Basic information

Entry
Database: PDB / ID: 8h5t
TitleCrystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-015
Components
  • Nanobody Nb-015
  • Spike protein S1
KeywordsVIRAL PROTEIN / IMMUNE SYSTEM
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / 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 / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, J. / Lin, S. / Lu, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Pathog. / Year: 2023
Title: Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization.
Authors: Yang, J. / Lin, S. / Chen, Z. / Yang, F. / Guo, L. / Wang, L. / Duan, Y. / Zhang, X. / Dai, Y. / Yin, K. / Yu, C. / Yuan, X. / Sun, H. / He, B. / Cao, Y. / Ye, H. / Dong, H. / Liu, X. / ...Authors: Yang, J. / Lin, S. / Chen, Z. / Yang, F. / Guo, L. / Wang, L. / Duan, Y. / Zhang, X. / Dai, Y. / Yin, K. / Yu, C. / Yuan, X. / Sun, H. / He, B. / Cao, Y. / Ye, H. / Dong, H. / Liu, X. / Chen, B. / Li, J. / Zhao, Q. / Lu, G.
History
DepositionOct 13, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
B: Nanobody Nb-015
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0053
Polymers38,7832
Non-polymers2211
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.816, 75.816, 119.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Spike protein S1


Mass: 24501.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#2: Antibody Nanobody Nb-015


Mass: 14281.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Brevibacillus choshinensis (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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium formate, pH 7.2, 20% 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: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22938 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 46.136
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.664 / Num. unique obs: 2299

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YZ5, 5TP3

6yz5

5tp3


Resolution: 2→26.152 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1137 4.96 %
Rwork0.1711 21780 -
obs0.1727 22917 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.56 Å2 / Biso mean: 45.28 Å2 / Biso min: 22.15 Å2
Refinement stepCycle: final / Resolution: 2→26.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 14 146 2566
Biso mean--69.29 45.94 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072486
X-RAY DIFFRACTIONf_angle_d0.853371
X-RAY DIFFRACTIONf_chiral_restr0.053351
X-RAY DIFFRACTIONf_plane_restr0.005433
X-RAY DIFFRACTIONf_dihedral_angle_d13.0761448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.08740.25111540.19562671
2.0874-2.19730.26831200.18672740
2.1973-2.33490.21921470.19752704
2.3349-2.51510.23881520.18592729
2.5151-2.76790.23831570.18782706
2.7679-3.16790.19471260.17882732
3.1679-3.98890.20441240.1622758
3.9889-26.1520.17871570.15852740
Refinement TLS params.Method: refined / Origin x: -2.9867 Å / Origin y: 15.2311 Å / Origin z: -0.6199 Å
111213212223313233
T0.2676 Å20.0159 Å20.0119 Å2-0.2126 Å2-0.0394 Å2--0.2292 Å2
L1.4633 °20.2001 °2-0.1107 °2-0.7378 °2-0.2509 °2--0.9812 °2
S0.015 Å °-0.0815 Å °0.1017 Å °-0.1327 Å °-0.0428 Å °0.0419 Å °0.0023 Å °0.0323 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA335 - 527
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allB2 - 120
4X-RAY DIFFRACTION1allS1 - 146

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