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- PDB-8eoz: Precisely patterned nanofibers made from extendable protein multi... -

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Basic information

Entry
Database: PDB / ID: 8eoz
TitlePrecisely patterned nanofibers made from extendable protein multiplexes
ComponentsC3HR3_4r
KeywordsDE NOVO PROTEIN / de novo design / nanofibers
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBera, A.K. / Bethel, N.P. / Kang, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Chem / Year: 2023
Title: Precisely patterned nanofibres made from extendable protein multiplexes.
Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb ...Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb / Xinting Li / Banumathi Sankaran / David Baker /
Abstract: Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the ...Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C to C and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
History
DepositionOct 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: C3HR3_4r


Theoretical massNumber of molelcules
Total (without water)28,2571
Polymers28,2571
Non-polymers00
Water00
1
B: C3HR3_4r

B: C3HR3_4r

B: C3HR3_4r


Theoretical massNumber of molelcules
Total (without water)84,7703
Polymers84,7703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5200 Å2
ΔGint-31 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.225, 68.225, 139.038
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein C3HR3_4r


Mass: 28256.770 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)

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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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole.HCl pH 8.0 15% (w/v) MPD; 5% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→46.35 Å / Num. obs: 4528 / % possible obs: 93.49 % / Redundancy: 1.3 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.95
Reflection shellResolution: 3→3.1 Å / Redundancy: 1 % / Mean I/σ(I) obs: 4.09 / Num. unique obs: 328 / CC1/2: 0.85 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed Model

Resolution: 3→46.35 Å / SU ML: 0.412 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 29.9348
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2867 459 10.14 %
Rwork0.2316 4068 -
obs0.2371 4527 93.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.31 Å2
Refinement stepCycle: LAST / Resolution: 3→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 0 0 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171900
X-RAY DIFFRACTIONf_angle_d0.43542548
X-RAY DIFFRACTIONf_chiral_restr0.0347292
X-RAY DIFFRACTIONf_plane_restr0.0019323
X-RAY DIFFRACTIONf_dihedral_angle_d13.5267757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.321390.27571232X-RAY DIFFRACTION85.26
3.1-4.330.30761640.23931454X-RAY DIFFRACTION99.69
4.33-46.350.2481560.20091382X-RAY DIFFRACTION95.53
Refinement TLS params.Method: refined / Origin x: 16.6259663416 Å / Origin y: -9.17202855309 Å / Origin z: -0.954964063269 Å
111213212223313233
T-0.412809364426 Å20.223652577852 Å2-0.118959353986 Å2-0.118623262739 Å20.0542297261676 Å2--0.0263808106575 Å2
L0.0959484769968 °20.0862041140841 °20.0132146268267 °2-0.213193917243 °20.0742119268052 °2--0.160063438471 °2
S0.0105483407571 Å °-0.0860178708451 Å °-0.201313844519 Å °0.389688944988 Å °-0.0455679916113 Å °-0.323763487463 Å °0.498432505027 Å °0.335975639306 Å °0.0571448765831 Å °
Refinement TLS groupSelection details: all

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