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- PDB-8idi: Crystal structure of nanobody VHH-T71 with MERS-CoV RBD -

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Basic information

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


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to 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, 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, 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, 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 speciesCamelus dromedarius (Arabian camel)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 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 23, 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: VHH-T71
B: Spike protein S1
C: VHH-T71
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2396
Polymers80,4174
Non-polymers1,8222
Water14,736818
1
A: VHH-T71
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1203
Polymers40,2092
Non-polymers9111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint9 kcal/mol
Surface area15950 Å2
MethodPISA
2
B: Spike protein S1
C: VHH-T71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1203
Polymers40,2092
Non-polymers9111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint12 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.549, 46.835, 95.946
Angle α, β, γ (deg.)90.00, 112.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody VHH-T71


Mass: 14950.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Homo sapiens (human)
#2: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 25258.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Gene: S / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R9UQ53
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[DManpa1-3][DManpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / 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: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 4% v/v Tacsimate, pH 6.0, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.901→36.551 Å / Num. obs: 77670 / % possible obs: 99.83 % / Redundancy: 6.4 % / CC1/2: 0.995 / Net I/σ(I): 21.16
Reflection shellResolution: 1.901→1.969 Å / Num. unique obs: 7647 / CC1/2: 0.869

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→36.551 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 3933 5.06 %
Rwork0.1729 --
obs0.1747 77659 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→36.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 122 818 6129
Refine LS restraintsType: f_bond_d / Dev ideal: 0.006 / Number: 5450
LS refinement shellResolution: 1.901→1.924 Å
RfactorNum. reflection% reflection
Rfree0.2739 161 -
Rwork0.2319 2525 -
obs--97 %
Refinement TLS params.Method: refined / Origin x: 68.4725 Å / Origin y: 48.5948 Å / Origin z: 48.427 Å
111213212223313233
T0.1691 Å2-0.0087 Å20.0014 Å2-0.1808 Å20.0272 Å2--0.1711 Å2
L0.1167 °20.0398 °2-0.0818 °2-0.0734 °20.0099 °2--0.0179 °2
S0.0256 Å °-0.0333 Å °0.0069 Å °0.0074 Å °-0.0302 Å °-0.0342 Å °0.0071 Å °0.0477 Å °0.0049 Å °
Refinement TLS groupSelection details: all

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