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- PDB-8wcg: Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR2... -

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Basic information

Entry
Database: PDB / ID: 8wcg
TitleCrystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347
Components
  • Spike protein S1
  • aSR29 nanobody
  • aSR347 nanobody
KeywordsANTIVIRAL PROTEIN / alpaca
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / 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 / 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 / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsZeng, W.H. / Ma, H. / Jin, T.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100745 China
National Natural Science Foundation of China (NSFC)82272301 China
CitationJournal: To Be Published
Title: Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347
Authors: Zeng, W.H. / Ma, H. / Jin, T.C.
History
DepositionSep 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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
C: aSR29 nanobody
B: Spike protein S1
D: aSR29 nanobody
b: aSR347 nanobody
E: aSR347 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3338
Polymers100,8916
Non-polymers4422
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-31 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.852, 134.679, 136.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spike protein S1


Mass: 22193.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: S, 2 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P59594
#2: Antibody aSR29 nanobody


Mass: 14081.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody aSR347 nanobody


Mass: 14170.683 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG4000, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 103.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979021 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979021 Å / Relative weight: 1
ReflectionResolution: 2.599→95.93 Å / Num. obs: 83452 / % possible obs: 99.1 % / Redundancy: 7.7 % / Biso Wilson estimate: 52.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.129 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.97 % / Rmerge(I) obs: 1.191 / Num. unique obs: 6390 / CC1/2: 0.784 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XSCALEdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→47.967 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 4176 5 %Random selection
Rwork0.2323 ---
obs0.2346 83452 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→47.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6983 0 30 98 7111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.6349826
X-RAY DIFFRACTIONf_dihedral_angle_d8.0894183
X-RAY DIFFRACTIONf_chiral_restr0.0761051
X-RAY DIFFRACTIONf_plane_restr0.0041281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.62830.371500.33452700X-RAY DIFFRACTION99
2.6283-2.65920.38961490.32182642X-RAY DIFFRACTION100
2.6592-2.69160.40071160.30622653X-RAY DIFFRACTION99
2.6916-2.72570.30231220.29912719X-RAY DIFFRACTION100
2.7257-2.76150.31021360.30862672X-RAY DIFFRACTION100
2.7615-2.79940.37931150.30562683X-RAY DIFFRACTION99
2.7994-2.83930.32751190.29752671X-RAY DIFFRACTION100
2.8393-2.88170.3871380.31112639X-RAY DIFFRACTION99
2.8817-2.92670.376940.30322712X-RAY DIFFRACTION99
2.9267-2.97470.36171440.30092649X-RAY DIFFRACTION100
2.9747-3.0260.39931420.29832679X-RAY DIFFRACTION100
3.026-3.0810.39121480.30982687X-RAY DIFFRACTION100
3.081-3.14030.40431490.28292629X-RAY DIFFRACTION99
3.2044-3.2740.37231300.27832654X-RAY DIFFRACTION100
3.274-3.35020.28071600.26582647X-RAY DIFFRACTION99
3.3502-3.43390.32171370.2662625X-RAY DIFFRACTION99
3.4339-3.52670.28182030.27632626X-RAY DIFFRACTION100
3.5267-3.63050.35061300.2632683X-RAY DIFFRACTION100
3.6305-3.74760.28041440.25092641X-RAY DIFFRACTION100
3.7476-3.88150.26821560.22392652X-RAY DIFFRACTION99
3.8815-4.03680.28541120.21732085X-RAY DIFFRACTION78
4.0368-4.22050.25451060.20132680X-RAY DIFFRACTION100
4.2205-4.44280.21381800.18242620X-RAY DIFFRACTION100
4.4428-4.7210.2261550.15822646X-RAY DIFFRACTION100
4.721-5.08510.16851460.16442665X-RAY DIFFRACTION100
5.0851-5.59610.26581600.19032646X-RAY DIFFRACTION100
5.5961-6.40430.25311370.20462671X-RAY DIFFRACTION100

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