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Basic information

Entry
Database: PDB / ID: 6xi6
TitleHierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks
Componentshelical fusion design
KeywordsDE NOVO PROTEIN / helical fusion / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsBera, A.K. / Hsia, Y. / Kang, A.S. / Shankaran, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) 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
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: helical fusion design


Theoretical massNumber of molelcules
Total (without water)30,7841
Polymers30,7841
Non-polymers00
Water23413
1
A: helical fusion design

A: helical fusion design

A: helical fusion design


Theoretical massNumber of molelcules
Total (without water)92,3513
Polymers92,3513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7840 Å2
ΔGint-46 kcal/mol
Surface area38370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.970, 101.970, 78.444
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
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-312-

HOH

31A-313-

HOH

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Components

#1: Protein helical fusion design


Mass: 30783.764 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.: 13 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 TrisCl pH 8.5. 10 % Glycerol and 25 (v/v) 1,2-Propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.69→38.48 Å / Num. obs: 8434 / % possible obs: 99.59 % / Redundancy: 4.8 % / Biso Wilson estimate: 66.23 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.4
Reflection shellResolution: 2.69→2.78 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 844 / CC1/2: 0.889 / % possible all: 99.41

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Processing

Software
NameVersionClassification
PHENIX1.17rc1_3605refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 2.69→38.48 Å / SU ML: 0.4574 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.2912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2772 848 10.08 %
Rwork0.221 7564 -
obs0.2268 8412 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.93 Å2
Refinement stepCycle: LAST / Resolution: 2.69→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 0 13 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012048
X-RAY DIFFRACTIONf_angle_d0.30572754
X-RAY DIFFRACTIONf_chiral_restr0.0273325
X-RAY DIFFRACTIONf_plane_restr0.0013374
X-RAY DIFFRACTIONf_dihedral_angle_d18.70751337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.860.42271400.3441243X-RAY DIFFRACTION99.5
2.86-3.080.32571440.28371283X-RAY DIFFRACTION99.58
3.08-3.390.3291410.24691264X-RAY DIFFRACTION99.72
3.39-3.880.24671410.21051252X-RAY DIFFRACTION99.93
3.88-4.880.26221380.20041266X-RAY DIFFRACTION99.86
4.89-38.480.25621440.20091256X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: -2.0444165613 Å / Origin y: -17.0662056822 Å / Origin z: -2.79114321318 Å
111213212223313233
T0.486259782217 Å20.0382960830698 Å2-0.121715114011 Å2-0.394695148218 Å2-0.0569523303322 Å2--0.501378556736 Å2
L0.806619603694 °20.497918881146 °2-0.319966194933 °2-1.14513135232 °2-0.866818875829 °2--4.51852300479 °2
S0.035755757006 Å °-0.183900752859 Å °-0.157193433671 Å °0.0874008030501 Å °-0.0857625598478 Å °-0.172261929293 Å °0.620180706041 Å °-0.272502459241 Å °0.0696768875605 Å °
Refinement TLS groupSelection details: all

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