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- PDB-7fat: Structure Determination of the RBD-NB1A7 -

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Basic information

Entry
Database: PDB / ID: 7fat
TitleStructure Determination of the RBD-NB1A7
Components
  • Spike protein S1
  • nb_1A7
KeywordsSTRUCTURAL PROTEIN / SARS-CoV-2 / RBD / nanobody
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 / 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 / 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
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsGeng, Y. / Shi, Z.Z. / Li, X.Y. / Wang, L. / Sun, Z.C. / Zhang, H.W. / Chen, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670743 China
CitationJournal: Structure / Year: 2022
Title: Structural basis of nanobodies neutralizing SARS-CoV-2 variants
Authors: Shi, Z. / Li, X. / Wang, L. / Sun, Z. / Zhang, H. / Chen, X. / Cui, Q. / Qiao, H. / Lan, Z. / Zhang, X. / Li, X. / Li, L. / Xu, J. / Gong, R. / Fan, C. / Geng, Y.
History
DepositionJul 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: nb_1A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8483
Polymers39,4242
Non-polymers4241
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-1 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.663, 183.795, 42.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11B-234-

HOH

21B-260-

HOH

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2
#2: Antibody nb_1A7


Mass: 14774.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 8% PEG6000, 0.1 M citric acid pH 3.5 and 2% ethylene glycol

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Data collection

DiffractionMean temperature: 97.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→19.72 Å / Num. obs: 27746 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 25.04 Å2 / CC1/2: 0.96 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 30986 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ch5

7ch5


Resolution: 1.99→19.72 Å / SU ML: 0.2696 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.0359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 1917 7.24 %
Rwork0.1927 24544 -
obs0.1963 26461 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.04 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 28 245 2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042526
X-RAY DIFFRACTIONf_angle_d1.0923425
X-RAY DIFFRACTIONf_chiral_restr0.0624363
X-RAY DIFFRACTIONf_plane_restr0.0069446
X-RAY DIFFRACTIONf_dihedral_angle_d6.1259364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.2933580.2338855X-RAY DIFFRACTION43.37
2.04-2.090.3196940.26341150X-RAY DIFFRACTION58.27
2.09-2.150.34021180.25191437X-RAY DIFFRACTION73.87
2.16-2.220.27411260.24651712X-RAY DIFFRACTION86.29
2.22-2.30.3681430.25961711X-RAY DIFFRACTION87.33
2.3-2.40.31241480.22441830X-RAY DIFFRACTION93.08
2.4-2.50.28871380.2251878X-RAY DIFFRACTION93.85
2.5-2.640.28641590.22911901X-RAY DIFFRACTION95.99
2.64-2.80.28051420.21861940X-RAY DIFFRACTION97.24
2.8-3.020.27721500.20731981X-RAY DIFFRACTION98.93
3.02-3.320.24651510.19231979X-RAY DIFFRACTION99.07
3.32-3.80.24071560.16852010X-RAY DIFFRACTION99.4
3.8-4.770.16031650.13372027X-RAY DIFFRACTION99.28
4.77-19.720.18621690.17592133X-RAY DIFFRACTION99.48

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