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- PDB-6xt4: C3_HD-1069 (1BH-69) - fusion protein of helical bundle and repeat... -

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Basic information

Entry
Database: PDB / ID: 6xt4
TitleC3_HD-1069 (1BH-69) - fusion protein of helical bundle and repeat protein
Components1BH_69
KeywordsDE NOVO PROTEIN / helical bundle repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBick, M.J. / Hsia, Y. / Sankaran, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1629214 United States
CitationJournal: Nat Commun / Year: 2021
Title: Design of multi-scale protein complexes by hierarchical building block fusion.
Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una ...Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una Nattermann / Evelyn Tsai / Ayesha Saleem / Cameron M Chow / Damian Ekiert / Gira Bhabha / David Veesler / David Baker /
Abstract: A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two ...A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1BH_69


Theoretical massNumber of molelcules
Total (without water)29,3801
Polymers29,3801
Non-polymers00
Water724
1
A: 1BH_69

A: 1BH_69

A: 1BH_69


Theoretical massNumber of molelcules
Total (without water)88,1393
Polymers88,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8990 Å2
ΔGint-98 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.313, 107.313, 56.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 1BH_69


Mass: 29379.666 Da / Num. of mol.: 1
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.: 4 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: JCSG+ condition D3 (0.2 M sodium chloride, 0.1 M sodium/potassium phosphate, pH 6.2, 50% v/v PEG200), no additional cryoprotection added

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen vapor stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9993 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9993 Å / Relative weight: 1
ReflectionResolution: 2.24→48.01 Å / Num. obs: 11562 / % possible obs: 100 % / Redundancy: 5.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.071 / Rrim(I) all: 0.167 / Net I/σ(I): 5.3 / Num. measured all: 64175 / Scaling rejects: 683
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.24-2.35.10.86541828140.8620.4420.9731.8100
10.02-48.015.80.1117461290.9880.0510.12213.299

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.12 Å48.01 Å
Translation4.12 Å48.01 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.8.2phasing
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
DIALS1.2.2-g62d8f5d-releasedata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 2.4→48.006 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 32.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 439 4.7 %
Rwork0.2253 8901 -
obs0.2273 9340 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.41 Å2 / Biso mean: 59.1155 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.4→48.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 4 1618
Biso mean---53.08 -
Num. residues----235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4001-2.74730.33351620.287289399
2.7473-3.46120.28971370.24683034100
3.4612-48.0060.24691400.2033297499

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