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- PDB-8g9k: Geometrically programmable nanomaterial construction using regula... -

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Entry
Database: PDB / ID: 8g9k
TitleGeometrically programmable nanomaterial construction using regularized protein building blocks
ComponentsTHR2
KeywordsDE NOVO PROTEIN / nanomaterial / protein building blocks / De novo design / train-track
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBera, A.K. / Huddy, T. / Baker, D. / Kang, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nature / Year: 2024
Title: Blueprinting extendable nanomaterials with standardized protein blocks.
Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / ...Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / Nicolas Coudray / S John Calise / Fatima A Davila-Hernandez / Hannah L Han / Kenneth D Carr / Zhe Li / Ryan McHugh / Gabriella Reggiano / Alex Kang / Banumathi Sankaran / Miles S Dickinson / Brian Coventry / T J Brunette / Yulai Liu / Justas Dauparas / Andrew J Borst / Damian Ekiert / Justin M Kollman / Gira Bhabha / David Baker /
Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.
History
DepositionFeb 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THR2
B: THR2


Theoretical massNumber of molelcules
Total (without water)43,9552
Polymers43,9552
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.394, 61.195, 149.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 THR2


Mass: 21977.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.3M Sodium nitrate, 0.3M Sodium phosphate dibasic, 0.3M Ammonium sulfate, 0.1M Sodium HEPES; MOPS(acid) pH 7.5, 30% mixture of 40% v/v Ethylene glycol; 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.48→56.61 Å / Num. obs: 15526 / % possible obs: 98.91 % / Redundancy: 7.4 % / Biso Wilson estimate: 53.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.025 / Net I/σ(I): 17.19
Reflection shellResolution: 2.48→2.56 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.123 / Num. unique obs: 1388 / CC1/2: 0.999 / Rpim(I) all: 0.491 / % possible all: 98.79

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
PHENIX1.18rc2_3793refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→56.61 Å / SU ML: 0.3404 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2994 1576 10.15 %
Rwork0.2622 13949 -
obs0.266 15525 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.5 Å2
Refinement stepCycle: LAST / Resolution: 2.48→56.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 39 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00132973
X-RAY DIFFRACTIONf_angle_d0.37594013
X-RAY DIFFRACTIONf_chiral_restr0.0276514
X-RAY DIFFRACTIONf_plane_restr0.0025518
X-RAY DIFFRACTIONf_dihedral_angle_d9.99521145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.560.3471590.31251228X-RAY DIFFRACTION98.72
2.56-2.650.35621160.29821245X-RAY DIFFRACTION98.05
2.65-2.760.37981590.31111235X-RAY DIFFRACTION99.57
2.76-2.880.29241190.27641264X-RAY DIFFRACTION99.64
2.88-3.040.36291590.31031231X-RAY DIFFRACTION98.93
3.04-3.230.39171190.29181279X-RAY DIFFRACTION98.73
3.23-3.470.28141580.24551250X-RAY DIFFRACTION99.02
3.47-3.820.281600.23871265X-RAY DIFFRACTION99.58
3.82-4.380.27531200.22251306X-RAY DIFFRACTION99.79
4.38-5.510.25791590.24291291X-RAY DIFFRACTION99.32
5.51-56.610.30861480.2891355X-RAY DIFFRACTION96.78
Refinement TLS params.Method: refined / Origin x: 11.722390804 Å / Origin y: 17.7500081448 Å / Origin z: 16.0646507424 Å
111213212223313233
T0.40990497238 Å2-0.00575590741785 Å2-0.0319477374425 Å2-0.378922920606 Å20.0818748915567 Å2--0.416886569449 Å2
L1.4331850866 °2-0.195084334297 °20.275215734045 °2-0.780746239331 °20.637695287011 °2--1.60925650139 °2
S-0.0303470472952 Å °-0.148058177526 Å °-0.373375380566 Å °0.125941532329 Å °-0.0279184411124 Å °0.00683948504922 Å °0.0689222727691 Å °-0.227399461114 Å °0.00129768793142 Å °
Refinement TLS groupSelection details: all

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