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- PDB-8qb3: ADDobody zinc containing condition -

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Basic information

Entry
Database: PDB / ID: 8qb3
TitleADDobody zinc containing condition
ComponentsADDobody
KeywordsVIRAL PROTEIN / Adenovirus capsid / Penton base protein / Structural viral protein
Biological speciesHuman adenovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBuzas, D. / Toelzer, C. / Berger, I. / Schaffitzel, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Structure / Year: 2024
Title: Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders.
Authors: Dora Buzas / Huan Sun / Christine Toelzer / Sathish K N Yadav / Ufuk Borucu / Gunjan Gautam / Kapil Gupta / Joshua C Bufton / Julien Capin / Richard B Sessions / Frederic Garzoni / Imre ...Authors: Dora Buzas / Huan Sun / Christine Toelzer / Sathish K N Yadav / Ufuk Borucu / Gunjan Gautam / Kapil Gupta / Joshua C Bufton / Julien Capin / Richard B Sessions / Frederic Garzoni / Imre Berger / Christiane Schaffitzel /
Abstract: Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based ...Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based therapeutics independent of a cold chain. To expand the scope of ADDomers for new applications, we engineered ADDobodies, representing PBP crown domain, genetically separated from PBP multimerization domain. We inserted heterologous sequences into hyper-variable loops, resulting in monomeric, thermostable ADDobodies expressed at high yields in Escherichia coli. The X-ray structure of an ADDobody prototype validated our design. ADDobodies can be used in ribosome display experiments to select a specific binder against a target, with an enrichment factor of ∼10-fold per round. ADDobodies can be re-converted into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2 Å electron cryo-microscopy structure. Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target.
History
DepositionAug 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADDobody
B: ADDobody
C: ADDobody
D: ADDobody
E: ADDobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,3086
Polymers176,2435
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-52 kcal/mol
Surface area47790 Å2
Unit cell
Length a, b, c (Å)101.478, 103.072, 167.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
ADDobody


Mass: 35248.512 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus sp. / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 6000, 0.1 M zinc-acetate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.9→87.74 Å / Num. obs: 75083 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 26.71 Å2 / CC1/2: 0.946 / Net I/σ(I): 5.6
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.136 / Num. unique obs: 39593

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→87.74 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2906 3763 5.02 %
Rwork0.2714 --
obs0.2724 74991 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→87.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 1 0 8617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d12.2393081
X-RAY DIFFRACTIONf_chiral_restr0.0431338
X-RAY DIFFRACTIONf_plane_restr0.0051553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.38041490.36632576X-RAY DIFFRACTION99
2.94-2.980.41961370.3512643X-RAY DIFFRACTION99
4.55-4.790.23451450.20822663X-RAY DIFFRACTION100
4.79-5.090.26141470.21782608X-RAY DIFFRACTION100
5.09-5.480.28541320.23982648X-RAY DIFFRACTION100
6.03-6.90.26921260.28532652X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 33.0606 Å / Origin y: 23.3463 Å / Origin z: 59.9577 Å
111213212223313233
T0.1238 Å20.0121 Å2-0.0114 Å2-0.1421 Å2-0.0477 Å2--0.1681 Å2
L0.5937 °2-0.3963 °20.2296 °2-1.4978 °2-0.5125 °2--0.806 °2
S-0.1178 Å °-0.0822 Å °0.0553 Å °0.4136 Å °0.0779 Å °-0.0679 Å °-0.1344 Å °0.0998 Å °0.0355 Å °
Refinement TLS groupSelection details: all

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