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- PDB-8uos: Designed IL-1R antagonist IL-1Rmb80 -

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Basic information

Entry
Database: PDB / ID: 8uos
TitleDesigned IL-1R antagonist IL-1Rmb80
ComponentsIL-1Rmb80
KeywordsDE NOVO PROTEIN / protein design / antagonist / immune system
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJude, K.M. / Garcia, K.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI51321 United States
Howard Hughes Medical Institute (HHMI) United States
The Mark Foundation United States
CitationJournal: Nat Commun / Year: 2024
Title: De novo design of miniprotein antagonists of cytokine storm inducers.
Authors: Huang, B. / Coventry, B. / Borowska, M.T. / Arhontoulis, D.C. / Exposit, M. / Abedi, M. / Jude, K.M. / Halabiya, S.F. / Allen, A. / Cordray, C. / Goreshnik, I. / Ahlrichs, M. / Chan, S. / ...Authors: Huang, B. / Coventry, B. / Borowska, M.T. / Arhontoulis, D.C. / Exposit, M. / Abedi, M. / Jude, K.M. / Halabiya, S.F. / Allen, A. / Cordray, C. / Goreshnik, I. / Ahlrichs, M. / Chan, S. / Tunggal, H. / DeWitt, M. / Hyams, N. / Carter, L. / Stewart, L. / Fuller, D.H. / Mei, Y. / Garcia, K.C. / Baker, D.
History
DepositionOct 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IL-1Rmb80
B: IL-1Rmb80
C: IL-1Rmb80
D: IL-1Rmb80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9465
Polymers30,8544
Non-polymers921
Water54030
1
A: IL-1Rmb80


Theoretical massNumber of molelcules
Total (without water)7,7131
Polymers7,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IL-1Rmb80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8062
Polymers7,7131
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IL-1Rmb80


Theoretical massNumber of molelcules
Total (without water)7,7131
Polymers7,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: IL-1Rmb80


Theoretical massNumber of molelcules
Total (without water)7,7131
Polymers7,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.343, 55.220, 53.875
Angle α, β, γ (deg.)90.000, 103.539, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
IL-1Rmb80


Mass: 7713.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.17 M Ammonium sulfate, 25.5% PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.96→36.9 Å / Num. obs: 16949 / % possible obs: 98.18 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1069 / Rpim(I) all: 0.04372 / Rrim(I) all: 0.1157 / Net I/σ(I): 9.75
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.405 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2831 / CC1/2: 0.46 / CC star: 0.794 / Rpim(I) all: 0.9199 / Rrim(I) all: 2.405 / % possible all: 98.29

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→36.9 Å / SU ML: 0.3658 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 844 4.99 %
Rwork0.1996 16053 -
obs0.2015 16897 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.8 Å2
Refinement stepCycle: LAST / Resolution: 1.96→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 6 30 1972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221979
X-RAY DIFFRACTIONf_angle_d0.45212659
X-RAY DIFFRACTIONf_chiral_restr0.0302273
X-RAY DIFFRACTIONf_plane_restr0.0026362
X-RAY DIFFRACTIONf_dihedral_angle_d14.1928774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.080.41431400.34952672X-RAY DIFFRACTION98.29
2.08-2.240.33441370.25422603X-RAY DIFFRACTION96.85
2.24-2.470.27821420.21642687X-RAY DIFFRACTION99.23
2.47-2.830.26131420.19412697X-RAY DIFFRACTION99.13
2.83-3.560.23281400.19312670X-RAY DIFFRACTION97.54
3.56-36.90.19081430.17672724X-RAY DIFFRACTION97.92
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)
12.747925187860.9158785692011.74049760374.840493500871.132758614884.749397927560.1783416531280.0199844282369-0.498865631597-0.38525365169-0.08857951606070.275814803237-0.221049725936-0.564109189363-0.04966129693470.4382026493880.06244224586820.003442174854990.364738685579-0.04493516462410.40702454953910.287439806913.446858884816.1752252957
28.42284465539-1.1564456685-0.6635189402836.01123319170.3491834103593.775211379830.08342574344340.2123987139951.12962243899-0.563471654921-0.000412799841893-0.474133721014-0.1470313794020.202310750646-0.1528104256410.3132773722160.03555275892960.04745267214450.2674463224960.000305630159660.33226570911510.101254345222.222162979514.9134789084
32.36742990539-2.057665185151.9000739184.190265529631.185957825965.82160151850.0764724025268-0.845659283988-0.01334741367350.4228918560330.04200941472470.3636578885770.526117572089-0.071913521525-0.1253462574980.385010959601-0.01075704872380.06364750553560.4181913917880.03412352923050.3264498747166.9575717247119.739255694625.3662077076
43.97770281099-1.88841630068-0.6214311949325.766864610591.402246673414.418701472920.06926156845190.25738283498-0.0933125075195-0.342535816110.130745546115-0.02259171413020.0425585200632-0.0395530338462-0.2039513169820.326372534434-0.0126961291943-0.01017463420910.2319308581130.01386339811920.217654476136.3760802609317.54860747941.9933727703
52.532649549870.416622059171.603876672425.30583184164-0.3604173256735.075083376120.167309672336-1.01058819951-0.3360273501890.70288500367-0.1346323309260.0891899782630.144147663286-0.2301702277890.03025309035640.4468409164120.05546789411790.01479286749010.4190901823530.03799761778360.3136786243233.6643920086820.281501855752.1381229889
63.69827567612-0.7300297855663.472358082357.37387796279-1.574174203474.064974779460.0196309031099-0.07532292232770.6402608516090.050279684993-0.1433524454430.248345969079-0.660254418555-0.1003005128540.1465061828640.3733233729720.0492843092710.01511338212920.3895924338290.00233858631520.298482674138.0782041390940.368244882619.7824313494
72.77999064988-0.2350591512381.967465691143.039503960570.5542249406427.985407563850.228271446137-0.089192914231-0.4618583842630.05913180335530.1509176868390.04536228138260.603273130749-0.0512770919695-0.3370093622810.2596213906280.004401157299970.002456944783440.299241585919-0.03294377092380.327516231477.5551356480131.361330612620.3095810304
82.78314932075-0.04672806769913.132668292486.35749413241-0.1221435993458.755753517380.08459210418020.205358097176-0.0299824361101-0.568050686705-0.133636245942-0.3045518306190.0236297200420.0983986620335-0.01969563527460.3570473962040.001922200277590.04650456032510.413763600381-0.01356147561210.33682466099112.443125512433.515037057910.5946606417
97.715323074970.8822742248112.035882831835.976474945721.975571361267.24934640879-0.105175413054-0.3844632591470.1542037515570.5371024487410.1850465560740.1951976857780.168660001846-0.0919754116758-0.05805570481280.334962390696-0.0007083834749810.03616729105370.263593781834-0.01892752413950.2615737524614.880116157536.36559859146.5068996205
102.61720340484-0.08389828874941.986384930454.15584893082-0.013584025444.350444514870.04301598464850.3905838651430.336789163238-0.225332622763-0.0367226808793-0.00993553218801-0.166349578161-0.0478693956847-0.04200129744810.39214937694-0.00676462565517-0.001690361994830.3270753414650.01125232835880.289262120988.660360695233.582236682636.7438426873
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 19 )AA1 - 191 - 19
22chain 'A' and (resid 20 through 39 )AA20 - 3920 - 39
33chain 'A' and (resid 40 through 58 )AA40 - 5840 - 58
44chain 'B' and (resid 1 through 39 )BB1 - 391 - 39
55chain 'B' and (resid 40 through 58 )BB40 - 5840 - 58
66chain 'C' and (resid 1 through 19 )CD1 - 191 - 19
77chain 'C' and (resid 20 through 39 )CD20 - 3920 - 39
88chain 'C' and (resid 40 through 58 )CD40 - 5840 - 58
99chain 'D' and (resid 1 through 39 )DE1 - 391 - 39
1010chain 'D' and (resid 40 through 58 )DE40 - 5840 - 58

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