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- PDB-8hr2: Ternary Crystal Complex Structure of RBD with NB1B5 and NB1C6 -

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Basic information

Entry
Database: PDB / ID: 8hr2
TitleTernary Crystal Complex Structure of RBD with NB1B5 and NB1C6
Components
  • NB1B5
  • NB1C6
  • Spike protein S1
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / RBD / nanobody / complex. / STRUCTURAL PROTEIN / STRUCTURAL 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 / suppression by virus 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSun, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Structure basis of two nanobodies neutralizing SARS-CoV-2 Omicron variant by targeting ultra-conservative epitopes.
Authors: Sun, Z. / Wang, L. / Li, L. / Sun, Y. / Zhang, D. / Zhou, S. / Li, Y. / Li, X. / Qiao, H. / Cui, Q. / Lan, Z. / Meng, X. / Xu, J. / Geng, Y. / Dai, Y.
History
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
B: NB1C6
C: NB1B5


Theoretical massNumber of molelcules
Total (without water)52,2333
Polymers52,2333
Non-polymers00
Water3,423190
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)89.522, 89.522, 125.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Spike protein S1


Mass: 24649.645 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): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody NB1C6


Mass: 13994.384 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Antibody NB1B5


Mass: 13588.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: 0.2 mM HEPES pH7.0;12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→66 Å / Num. obs: 39139 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 24.7
Reflection shellResolution: 1.94→2.04 Å / Num. unique obs: 3773 / CC1/2: 0.851

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Processing

SoftwareName: PHENIX / Version: v1.20.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CH5

7ch5


Resolution: 1.94→48.85 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1912 4.88 %
Rwork0.1908 --
obs0.1923 39206 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 190 3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143488
X-RAY DIFFRACTIONf_angle_d2.0674732
X-RAY DIFFRACTIONf_dihedral_angle_d17.56492
X-RAY DIFFRACTIONf_chiral_restr0.092484
X-RAY DIFFRACTIONf_plane_restr0.011622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.2721200.22862445X-RAY DIFFRACTION83
1.99-2.040.25291430.19962944X-RAY DIFFRACTION100
2.04-2.10.2833400.2302761X-RAY DIFFRACTION26
2.1-2.170.23371660.19362934X-RAY DIFFRACTION100
2.17-2.240.22261550.19932796X-RAY DIFFRACTION98
2.26-2.340.2265910.19332456X-RAY DIFFRACTION94
2.34-2.440.23891580.20512930X-RAY DIFFRACTION100
2.44-2.570.24731470.20242979X-RAY DIFFRACTION100
2.57-2.730.2441340.22252372X-RAY DIFFRACTION80
2.73-2.940.25331340.20182974X-RAY DIFFRACTION100
2.94-3.240.25861390.20993010X-RAY DIFFRACTION100
3.24-3.710.24711420.18312840X-RAY DIFFRACTION94
3.71-4.670.15791670.15672713X-RAY DIFFRACTION90
4.67-48.850.23271760.19433140X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -44.6792 Å / Origin y: 35.2852 Å / Origin z: 1.9616 Å
111213212223313233
T0.2701 Å2-0.021 Å2-0.0009 Å2-0.2045 Å2-0.0195 Å2--0.2106 Å2
L1.4126 °20.6202 °20.1334 °2-1.7322 °2-0.1501 °2--0.9225 °2
S0.0205 Å °-0.058 Å °0.2197 Å °0.1805 Å °-0.0932 Å °0.0434 Å °-0.1969 Å °0.0535 Å °0.0581 Å °
Refinement TLS groupSelection details: all

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