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Basic information

Entry
Database: PDB / ID: 8cuu
TitleAccurate computational design of genetically encoded 3D protein crystals
Components
  • F4132-1-0 chain A
  • F4132-1-0 chain B
KeywordsDE NOVO PROTEIN / DE NOVO DESIGN / genetically encoded / 3D protein crystals
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F4132-1-0 chain A
B: F4132-1-0 chain B


Theoretical massNumber of molelcules
Total (without water)34,6332
Polymers34,6332
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)289.613, 289.613, 289.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+1/4
#3: x+1/4,z+1/4,-y+1/4
#4: z+1/4,y+1/4,-x+1/4
#5: -z+1/4,y+1/4,x+1/4
#6: -y+1/4,x+1/4,z+1/4
#7: y+1/4,-x+1/4,z+1/4
#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+1/4,x+1/4,-z+1/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+1/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x,y+1/2,z+1/2
#26: x+1/4,-z+3/4,y+3/4
#27: x+1/4,z+3/4,-y+3/4
#28: z+1/4,y+3/4,-x+3/4
#29: -z+1/4,y+3/4,x+3/4
#30: -y+1/4,x+3/4,z+3/4
#31: y+1/4,-x+3/4,z+3/4
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y+1/4,x+3/4,-z+3/4
#44: -y+1/4,-x+3/4,-z+3/4
#45: z+1/4,-y+3/4,x+3/4
#46: -z+1/4,-y+3/4,-x+3/4
#47: -x+1/4,z+3/4,y+3/4
#48: -x+1/4,-z+3/4,-y+3/4
#49: x+1/2,y,z+1/2
#50: x+3/4,-z+1/4,y+3/4
#51: x+3/4,z+1/4,-y+3/4
#52: z+3/4,y+1/4,-x+3/4
#53: -z+3/4,y+1/4,x+3/4
#54: -y+3/4,x+1/4,z+3/4
#55: y+3/4,-x+1/4,z+3/4
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+3/4,x+1/4,-z+3/4
#68: -y+3/4,-x+1/4,-z+3/4
#69: z+3/4,-y+1/4,x+3/4
#70: -z+3/4,-y+1/4,-x+3/4
#71: -x+3/4,z+1/4,y+3/4
#72: -x+3/4,-z+1/4,-y+3/4
#73: x+1/2,y+1/2,z
#74: x+3/4,-z+3/4,y+1/4
#75: x+3/4,z+3/4,-y+1/4
#76: z+3/4,y+3/4,-x+1/4
#77: -z+3/4,y+3/4,x+1/4
#78: -y+3/4,x+3/4,z+1/4
#79: y+3/4,-x+3/4,z+1/4
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+3/4,x+3/4,-z+1/4
#92: -y+3/4,-x+3/4,-z+1/4
#93: z+3/4,-y+3/4,x+1/4
#94: -z+3/4,-y+3/4,-x+1/4
#95: -x+3/4,z+3/4,y+1/4
#96: -x+3/4,-z+3/4,-y+1/4

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Components

#1: Protein F4132-1-0 chain A


Mass: 20118.365 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 F4132-1-0 chain B


Mass: 14514.650 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: 7.31 Å3/Da / Density % sol: 83.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.75 M NaCl

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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: Oct 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.91→167.21 Å / Num. obs: 23419 / % possible obs: 100 % / Redundancy: 78.2 % / Biso Wilson estimate: 104.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.027 / Net I/σ(I): 26.2
Reflection shellResolution: 2.91→3.09 Å / Rmerge(I) obs: 6.326 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3710 / CC1/2: 0.505 / Rpim(I) all: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Design Model

Resolution: 2.91→102.39 Å / SU ML: 0.3288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 1103 4.72 %
Rwork0.1895 22280 -
obs0.1902 23383 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.63 Å2
Refinement stepCycle: LAST / Resolution: 2.91→102.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 0 0 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832288
X-RAY DIFFRACTIONf_angle_d1.01653116
X-RAY DIFFRACTIONf_chiral_restr0.0553381
X-RAY DIFFRACTIONf_plane_restr0.0086401
X-RAY DIFFRACTIONf_dihedral_angle_d16.6651864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.040.35171440.31162684X-RAY DIFFRACTION99.61
3.04-3.20.30871290.27792748X-RAY DIFFRACTION100
3.2-3.40.28281280.24272736X-RAY DIFFRACTION100
3.4-3.670.22321230.20582759X-RAY DIFFRACTION100
3.67-4.030.23281410.19422743X-RAY DIFFRACTION100
4.04-4.620.18481280.1672792X-RAY DIFFRACTION100
4.62-5.820.18361540.16942809X-RAY DIFFRACTION100
5.82-102.390.17351560.1793009X-RAY DIFFRACTION100
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)
13.72880504281.51086583997-0.7396691814014.17066435576-1.105607656876.34241579985-0.04953531734220.0871759011814-0.323999296976-0.3750020020830.06747606888720.576355454520.4359237234540.143236369265-0.02580497926430.7389152714960.105901578058-0.08883270440330.7808012017150.07207492400691.03175734326-42.97726749128.25902210772-32.6324489841
22.437721624981.919185422090.2559799618333.91768818548-1.170081001853.922900457580.1728484429780.125260195237-0.5917076187410.08393954617830.1026202433020.1779454307790.16412045710.1446793702110.05516833533460.7122283042480.158246874492-0.07693314271010.8683590764040.05514940144070.85218726346-38.655331388714.8267376917-34.3181566811
33.864497381323.776844472140.01698452999664.88969398823-0.03175045268869.08254480274-0.6875794263260.7959425001190.08901684646910.4414918558070.0189754792915-0.6793433397780.1445851478740.8181392540090.1179546243180.8343973367040.0447921837787-0.08627772111640.9110649243530.1961696581080.989572090802-31.044010546219.3821110727-27.1120549633
42.008815649030.872870072496-2.736900504435.278235593012.100555559376.945385940920.0333475524746-0.276951387956-1.316646739710.4866488310250.706406911365-0.8709891634550.4752835442910.9185732703430.1399908325180.8224290739610.130442388194-0.2196324880671.135585690990.07794830577211.1709623789-23.612315506815.6223150999-32.066370948
54.256975347281.29846379295-0.5696457658115.08638602034-0.2258737028965.362529521440.0279289161285-0.145289428959-0.6517039958780.691846343319-0.0941880700013-0.0665761708760.4076990355190.2605095084440.02928636817420.8616227551930.0740398712253-0.02575718922210.7876342589250.1386636827611.07462349586-38.516471701412.2478723448-18.8987877987
62.06520650789-0.4072674664550.7101018316965.990532311510.6744928862364.122339592670.02771853791860.571411931690.456329463504-0.09484998065170.132564020710.750388724504-0.275564723273-0.159333157711-0.04067030723860.6733156361370.1315415352430.04946094252830.919695161310.2008533544211.04439646749-30.902623984-12.3954780859-27.7189096477
74.11488030423-2.065196541140.4554872336096.00604475813-0.1606712126074.47465725594-0.337264535432-0.7412707097790.7204382012710.8131178978230.3168763361721.552439594450.110914545233-0.947725353467-0.09545996694730.837502672347-0.00123691537590.2554217224770.9259022028240.07328105582331.16226821038-34.9541120687-15.8342728545-20.536016857
81.45737390117-0.985683379420.2693622755414.339146349440.07269147421133.309636251420.1787006760630.6558040799540.33675536692-0.5077941369760.0527581317219-0.59612006119-0.334797907390.322766517723-0.1206247769730.6772523791950.001551991461510.03576398279350.912245680120.2508093820590.98307311433-21.5383560091-13.6349674778-27.9318715073
94.42573917519-3.441109121571.753636648777.64101579483-0.4340362323152.00017695081-0.2002128312491.53750819821-0.0411058319384-1.49462149684-0.3139915430130.4057356437270.695007957073-0.282593561759-0.1559830779591.23257622269-0.000312595926757-0.01203125553091.54933358257-0.1659933555121.07438657948-31.3714681036-24.9805292073-43.6970958539
107.33568751167-2.91356296769-5.322239667824.310576610313.035852070034.67535038939-0.309045518651-0.5496255869151.864612767830.2182511031930.03114054147632.23392506965-0.953098963318-0.454982196729-0.5127767051720.788669455835-0.108386830922-0.1177740471340.7796887700110.4185291339910.247330777083-18.3566517719-13.6222652304-40.5313614225
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 61 )AA1 - 611 - 61
22chain 'A' and (resid 62 through 81 )AA62 - 8162 - 81
33chain 'A' and (resid 82 through 108 )AA82 - 10882 - 108
44chain 'A' and (resid 109 through 118 )AA109 - 118109 - 118
55chain 'A' and (resid 119 through 171 )AA119 - 171119 - 171
66chain 'B' and (resid 1 through 57 )BB1 - 571 - 57
77chain 'B' and (resid 58 through 76 )BB58 - 7658 - 76
88chain 'B' and (resid 77 through 95 )BB77 - 9577 - 95
99chain 'B' and (resid 96 through 102 )BB96 - 10296 - 102
1010chain 'B' and (resid 103 through 125 )BB103 - 125103 - 125

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