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Basic information

Entry
Database: PDB / ID: 6xns
TitleC3_crown-05
ComponentsC3_crown-05
KeywordsDE NOVO PROTEIN / HELICAL BUNDLE REPEAT PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 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 4, 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

Downloads & links

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Assembly

Deposited unit
A: C3_crown-05
B: C3_crown-05
C: C3_crown-05
D: C3_crown-05
E: C3_crown-05
F: C3_crown-05


Theoretical massNumber of molelcules
Total (without water)228,9346
Polymers228,9346
Non-polymers00
Water00
1
A: C3_crown-05
B: C3_crown-05
C: C3_crown-05


  • defined by author&software
  • Evidence: gel filtration, Assembly elutes at the expected volume under Superdex 200 Increase 10/300 GL (Cytiva)., mass spectrometry, Native mass spectrometry suggests trimeric formation in solution., ...Evidence: gel filtration, Assembly elutes at the expected volume under Superdex 200 Increase 10/300 GL (Cytiva)., mass spectrometry, Native mass spectrometry suggests trimeric formation in solution., light scattering, Dynamic light scattering (Wyatt) shows a monodisperse RH reflective of the design.
  • 114 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)114,4673
Polymers114,4673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-65 kcal/mol
Surface area47740 Å2
MethodPISA
2
D: C3_crown-05
E: C3_crown-05
F: C3_crown-05


Theoretical massNumber of molelcules
Total (without water)114,4673
Polymers114,4673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-66 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.135, 145.250, 161.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
C3_crown-05


Mass: 38155.633 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)

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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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: JCSG core I condition E11 (0.1M MES pH 5.0, 20% MPD) plus an additional 20% MPD as a cryoprotectant.

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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: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2018
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.19→48.69 Å / Num. obs: 44776 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.035 / Rrim(I) all: 0.105 / Net I/σ(I): 12.2 / Num. measured all: 396324 / Scaling rejects: 23
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
3.19-3.3192.8634212946610.2461.0063.0380.9100
11.94-48.697.40.03669909500.9990.0140.03945.297.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.31 Å48.69 Å
Translation5.31 Å48.69 Å

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHASER2.8.2phasing
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSJun 17, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 3.19→48.627 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 2000 4.48 %
Rwork0.2708 42677 -
obs0.272 44677 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 315.51 Å2 / Biso mean: 140.2386 Å2 / Biso min: 59.72 Å2
Refinement stepCycle: final / Resolution: 3.19→48.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12559 0 0 0 12559
Num. residues----1973
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.19-3.26980.4191400.4113299099
3.2698-3.35820.36561410.40853010100
3.3582-3.4570.41631430.38673031100
3.457-3.56850.43871390.38372973100
3.5685-3.6960.34881420.37043029100
3.696-3.84390.34841420.34733032100
3.8439-4.01880.38831420.35253031100
4.0188-4.23060.33891410.32813018100
4.2306-4.49540.34081430.30473050100
4.4954-4.84230.30831420.26053037100
4.8423-5.3290.35231440.30233061100
5.329-6.09880.35051430.35963078100
6.0988-7.6790.29931460.26243118100
7.679-48.6270.18391520.1671321999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0555-0.3752-0.9562.4077-0.16920.66750.03260.2376-0.1212-0.25010.1480.4010.5561-0.04560.11730.6786-0.13630.11190.71320.04840.649928.77188.160833.5713
21.2751-0.6707-0.38521.02510.91860.7341-0.15040.23460.0051-0.247-0.14160.44220.1395-0.1521-0.07150.7987-0.0922-0.05320.7436-0.07751.0314-0.40735.423931.2668
30.72630.3960.17230.5876-0.37770.5799-0.0726-0.06580.00110.1490.09140.16850.1497-0.0495-00.81430.10510.1550.6742-0.03940.797513.579522.729866.0197
40.3175-0.9180.52691.51180.68291.55580.10840.09150.2714-0.0750.1539-0.1347-0.3165-0.12830.19310.5099-0.2049-0.08990.57250.01660.603628.597566.45230.149
51.1743-0.6808-0.01121.3193-1.16190.6092-0.15510.14190.1821-0.0035-0.1833-0.2888-0.06520.28150.00240.7762-0.03280.05150.7390.01940.844457.53739.147932.2727
60.9397-1.1467-0.03530.93880.59260.6478-0.1859-0.02250.19410.1011-0.0424-0.3684-0.21870.1273-0.02440.8588-0.0204-0.20960.77350.08270.849942.086453.811765.6646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 330)A1 - 330
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 333)B0 - 333
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 329)C0 - 329
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 331)D1 - 331
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 328)E1 - 328
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 329)F3 - 329

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