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- PDB-8idm: Crystal structure of nanobody VHH-227 with nanobody VHH-T71 and M... -

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Basic information

Entry
Database: PDB / ID: 8idm
TitleCrystal structure of nanobody VHH-227 with nanobody VHH-T71 and MERS-CoV RBD
Components
  • Spike protein S1
  • VHH-227
  • VHH-T71
KeywordsVIRAL PROTEIN / MERS-CoV / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Similarity search - Domain/homology
Biological speciesCamelus dromedarius (Arabian camel)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsWang, X. / Tian, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Definition of a Novel Nanobody Binding Site specifically targeting the MERS-CoV RBD Core-Domain with Neutralizing Capacity
Authors: Idoudi, F. / Wang, R. / Tian, L. / Zhang, L. / Wang, X.
History
DepositionFeb 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
B: VHH-227
A: VHH-T71
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9046
Polymers54,8913
Non-polymers1,0133
Water00
1
B: VHH-227
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1372
Polymers14,7691
Non-polymers3671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VHH-T71


Theoretical massNumber of molelcules
Total (without water)14,8631
Polymers14,8631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9043
Polymers25,2581
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.440, 104.440, 318.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules D

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


Mass: 25258.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R9UQ53

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Antibody , 2 types, 2 molecules BA

#1: Antibody VHH-227


Mass: 14769.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Homo sapiens (human)
#2: Antibody VHH-T71


Mass: 14863.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Homo sapiens (human)

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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 genetically manipulated 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
#6: 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.: 1 / 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

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Details

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: 4.93 Å3/Da / Density % sol: 75.07 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 30% v/v PEGmme 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.59→16.22 Å / Num. obs: 12591 / % possible obs: 97.87 % / Redundancy: 16 % / CC1/2: 1 / Net I/σ(I): 14.2
Reflection shellResolution: 3.59→3.717 Å / Num. unique obs: 1193 / CC1/2: 0.606

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.59→16.22 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 593 4.73 %
Rwork0.2534 --
obs0.2543 12539 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.59→16.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 66 0 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043715
X-RAY DIFFRACTIONf_angle_d0.8195057
X-RAY DIFFRACTIONf_dihedral_angle_d11.68545
X-RAY DIFFRACTIONf_chiral_restr0.051581
X-RAY DIFFRACTIONf_plane_restr0.005641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.940.41091360.36692870X-RAY DIFFRACTION98
3.94-4.50.30971440.32922X-RAY DIFFRACTION99
4.5-5.630.25191580.25532978X-RAY DIFFRACTION100
5.63-16.220.25121550.21993176X-RAY DIFFRACTION100

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