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- PDB-7jvb: Crystal structure of the SARS-CoV-2 spike receptor-binding domain... -

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Basic information

Entry
Database: PDB / ID: 7jvb
TitleCrystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20
Components
  • Nanobody Nb20
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / COVID-19 / nanobody / spike protein / receptor-binding domain
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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 / symbiont entry into host cell / 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, 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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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, 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.287 Å
AuthorsXiang, Y. / Xiao, Z. / Liu, H. / Sang, Z. / Schneidman-Duhovny, D. / Zhang, C. / Shi, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128641 United States
CitationJournal: Science / Year: 2020
Title: Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2.
Authors: Xiang, Y. / Nambulli, S. / Xiao, Z. / Liu, H. / Sang, Z. / Duprex, W.P. / Schneidman-Duhovny, D. / Zhang, C. / Shi, Y.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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

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Assembly

Deposited unit
A: Spike protein S1
C: Nanobody Nb20
B: Spike protein S1
D: Nanobody Nb20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0138
Polymers75,4654
Non-polymers5484
Water00
1
A: Spike protein S1
C: Nanobody Nb20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0064
Polymers37,7322
Non-polymers2742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
D: Nanobody Nb20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0064
Polymers37,7322
Non-polymers2742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.716, 70.716, 435.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 25179.389 Da / Num. of mol.: 2
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 Nanobody Nb20


Mass: 12553.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 1 M sodium citrate

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.287→38.96 Å / Num. obs: 17442 / % possible obs: 96.34 % / Redundancy: 6.2 % / Biso Wilson estimate: 98.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.108 / Net I/σ(I): 7.8
Reflection shellResolution: 3.287→3.405 Å / Rmerge(I) obs: 0.591 / Num. unique obs: 1391 / CC1/2: 0.811 / Rpim(I) all: 0.445

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WAQ

6waq


Resolution: 3.287→38.959 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3222 870 5.02 %
Rwork0.2813 --
obs0.2834 17335 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.287→38.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 27 0 4748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054865
X-RAY DIFFRACTIONf_angle_d1.6636617
X-RAY DIFFRACTIONf_dihedral_angle_d16.0921716
X-RAY DIFFRACTIONf_chiral_restr0.054713
X-RAY DIFFRACTIONf_plane_restr0.004861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2875-3.49330.37031220.34872313X-RAY DIFFRACTION84
3.4933-3.76280.33781430.31872714X-RAY DIFFRACTION98
3.7628-4.14110.3121460.29682763X-RAY DIFFRACTION99
4.1411-4.73940.29511460.25392782X-RAY DIFFRACTION99
4.7394-5.96770.32031510.27272843X-RAY DIFFRACTION100
5.9677-38.9590.32541620.2733050X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.1778 Å / Origin y: -15.3348 Å / Origin z: -27.1171 Å
111213212223313233
T0.8428 Å2-0.3202 Å20.1095 Å2-1.0227 Å2-0.02 Å2--0.4437 Å2
L1.3738 °2-0.55 °2-0.2263 °2-0.5598 °20.4366 °2--1.2292 °2
S0.0208 Å °0.2411 Å °-0.1372 Å °0.1075 Å °-0.1789 Å °0.1076 Å °-0.0376 Å °-0.1693 Å °0.1663 Å °
Refinement TLS groupSelection details: all

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