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Basic information

Entry
Database: PDB / ID: 8cut
TitleAccurate computational design of genetically encoded 3D protein crystals
Components
  • I432-1(Imd) Chain A
  • I432-1(Imd) Chain B
KeywordsDE NOVO PROTEIN / DE NOVO DESIGN / genetically encoded / 3D protein crystals
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBera, A.K. / Li, Z. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Mater / Year: 2023
Title: Accurate computational design of three-dimensional protein crystals.
Authors: Zhe Li / Shunzhi Wang / Una Nattermann / Asim K Bera / Andrew J Borst / Muammer Y Yaman / Matthew J Bick / Erin C Yang / William Sheffler / Byeongdu Lee / Soenke Seifert / Greg L Hura / ...Authors: Zhe Li / Shunzhi Wang / Una Nattermann / Asim K Bera / Andrew J Borst / Muammer Y Yaman / Matthew J Bick / Erin C Yang / William Sheffler / Byeongdu Lee / Soenke Seifert / Greg L Hura / Hannah Nguyen / Alex Kang / Radhika Dalal / Joshua M Lubner / Yang Hsia / Hugh Haddox / Alexis Courbet / Quinton Dowling / Marcos Miranda / Andrew Favor / Ali Etemadi / Natasha I Edman / Wei Yang / Connor Weidle / Banumathi Sankaran / Babak Negahdari / Michael B Ross / David S Ginger / David Baker /
Abstract: Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing ...Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: I432-1(Imd) Chain A
B: I432-1(Imd) Chain B


Theoretical massNumber of molelcules
Total (without water)39,6572
Polymers39,6572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-8 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.478, 236.478, 236.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Space group name HallI423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x+1/2,y+1/2,z+1/2
#26: x+1/2,-z+1/2,y+1/2
#27: x+1/2,z+1/2,-y+1/2
#28: z+1/2,y+1/2,-x+1/2
#29: -z+1/2,y+1/2,x+1/2
#30: -y+1/2,x+1/2,z+1/2
#31: y+1/2,-x+1/2,z+1/2
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1/2,x+1/2
#35: z+1/2,-x+1/2,-y+1/2
#36: -y+1/2,z+1/2,-x+1/2
#37: -z+1/2,-x+1/2,y+1/2
#38: -z+1/2,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1/2
#40: x+1/2,-y+1/2,-z+1/2
#41: -x+1/2,y+1/2,-z+1/2
#42: -x+1/2,-y+1/2,z+1/2
#43: y+1/2,x+1/2,-z+1/2
#44: -y+1/2,-x+1/2,-z+1/2
#45: z+1/2,-y+1/2,x+1/2
#46: -z+1/2,-y+1/2,-x+1/2
#47: -x+1/2,z+1/2,y+1/2
#48: -x+1/2,-z+1/2,-y+1/2

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Components

#1: Protein I432-1(Imd) Chain A


Mass: 16310.777 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: Protein I432-1(Imd) Chain B


Mass: 23346.396 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)
Has protein modificationY

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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: 6.95 Å3/Da / Density % sol: 82.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25 mM Tris-HCl, 150 mM NaCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4→167.06 Å / Num. obs: 31391 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 70.14 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.056 / Net I/σ(I): 6.8
Reflection shellResolution: 4→4.41 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4680 / CC1/2: 0.414 / Rpim(I) all: 1.464

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Processing

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

Resolution: 4→48.27 Å / SU ML: 0.3741 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.8922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 1742 10 %
Rwork0.1872 15670 -
obs0.1909 17412 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.57 Å2
Refinement stepCycle: LAST / Resolution: 4→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 0 0 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172601
X-RAY DIFFRACTIONf_angle_d0.38823510
X-RAY DIFFRACTIONf_chiral_restr0.038415
X-RAY DIFFRACTIONf_plane_restr0.0029441
X-RAY DIFFRACTIONf_dihedral_angle_d12.0766971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.120.298910.2623823X-RAY DIFFRACTION60.81
4.12-4.250.24861410.2481308X-RAY DIFFRACTION97.12
4.25-4.40.29251500.21391369X-RAY DIFFRACTION100
4.4-4.580.20591490.19491330X-RAY DIFFRACTION100
4.58-4.790.25871540.1831373X-RAY DIFFRACTION99.93
4.79-5.040.22861520.18331346X-RAY DIFFRACTION99.93
5.04-5.350.22391510.18361337X-RAY DIFFRACTION99.87
5.36-5.770.22631570.20541362X-RAY DIFFRACTION99.87
5.77-6.340.2571470.20721344X-RAY DIFFRACTION99.87
6.35-7.260.22611560.161359X-RAY DIFFRACTION100
7.26-9.140.16181460.14821356X-RAY DIFFRACTION99.87
9.16-48.270.1721480.14861363X-RAY DIFFRACTION99.34

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