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Basic information

Entry
Database: PDB / ID: 6xh5
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
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsBera, A.K. / Hsia, Y. / Kang, A.S. / 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 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: helical fusion design
B: helical fusion design
C: helical fusion design
D: helical fusion design
E: helical fusion design
F: helical fusion design


Theoretical massNumber of molelcules
Total (without water)234,7206
Polymers234,7206
Non-polymers00
Water82946
1
A: helical fusion design
B: helical fusion design
C: helical fusion design


Theoretical massNumber of molelcules
Total (without water)117,3603
Polymers117,3603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-30 kcal/mol
Surface area44230 Å2
MethodPISA
2
D: helical fusion design
E: helical fusion design
F: helical fusion design


Theoretical massNumber of molelcules
Total (without water)117,3603
Polymers117,3603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-29 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.766, 166.766, 223.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
helical fusion design


Mass: 39119.957 Da / Num. of mol.: 6
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.: 46 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 Na-acetate pH 4.5 and 2.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.32→78.12 Å / Num. obs: 47181 / % possible obs: 99.86 % / Redundancy: 27.2 % / Biso Wilson estimate: 116.55 Å2 / CC1/2: 0.986 / Rpim(I) all: 0.0463 / Net I/σ(I): 17.98
Reflection shellResolution: 3.32→3.43 Å / Mean I/σ(I) obs: 2.09 / Num. unique obs: 4621 / CC1/2: 0.723 / Rpim(I) all: 0.3488 / % possible all: 28.4

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 3.32→78.12 Å / SU ML: 0.4571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2648 2333 4.95 %
Rwork0.2194 44808 -
obs0.2217 47141 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.39 Å2
Refinement stepCycle: LAST / Resolution: 3.32→78.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15834 0 0 49 15883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002215990
X-RAY DIFFRACTIONf_angle_d0.45721526
X-RAY DIFFRACTIONf_chiral_restr0.03962557
X-RAY DIFFRACTIONf_plane_restr0.00322805
X-RAY DIFFRACTIONf_dihedral_angle_d14.95766112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.390.38291160.30262607X-RAY DIFFRACTION99.96
3.39-3.460.35051230.29082582X-RAY DIFFRACTION99.96
3.46-3.540.34291660.2752570X-RAY DIFFRACTION99.96
3.54-3.630.32981300.28192603X-RAY DIFFRACTION99.96
3.63-3.730.30351420.29162605X-RAY DIFFRACTION99.93
3.73-3.840.29171250.25042589X-RAY DIFFRACTION99.89
3.84-3.960.33171330.24832615X-RAY DIFFRACTION99.85
3.96-4.10.28181300.23832625X-RAY DIFFRACTION100
4.1-4.270.26431610.21092594X-RAY DIFFRACTION100
4.27-4.460.23481370.20062613X-RAY DIFFRACTION99.96
4.46-4.70.24921220.19712631X-RAY DIFFRACTION99.93
4.7-4.990.23851270.21032653X-RAY DIFFRACTION99.96
4.99-5.380.27681560.21642635X-RAY DIFFRACTION99.93
5.38-5.920.29931340.23772652X-RAY DIFFRACTION100
5.92-6.770.32651700.24382654X-RAY DIFFRACTION100
6.77-8.530.2061180.18472739X-RAY DIFFRACTION99.93
8.53-78.120.21521430.18812841X-RAY DIFFRACTION98.81
Refinement TLS params.Method: refined / Origin x: -18.1497037018 Å / Origin y: -16.0583704885 Å / Origin z: 55.7190702377 Å
111213212223313233
T0.584392451107 Å20.0124306437133 Å20.0238750413252 Å2-0.582403439743 Å2-0.0274677797757 Å2--0.564944869945 Å2
L0.708606805067 °20.222660932217 °2-0.21555166219 °2-0.687305757079 °20.0255424919038 °2--0.955946245849 °2
S-0.147526028318 Å °-0.126301173106 Å °-0.135777076342 Å °-0.218615001839 Å °-0.109250092081 Å °0.0560178904121 Å °0.06929449391 Å °-0.117914735575 Å °0.229360807799 Å °
Refinement TLS groupSelection details: all

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