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- PDB-8u7c: Engineered NEMO minimal IKK-binding domain -

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Basic information

Entry
Database: PDB / ID: 8u7c
TitleEngineered NEMO minimal IKK-binding domain
ComponentsEngineered NEMO minimal IKK-binding domain
KeywordsIMMUNE SYSTEM / coiled-coil / scaffold protein
Function / homologypentane-1,5-diol / ERBIUM (III) ION / PROLINE / TERBIUM(III) ION / YTTRIUM (III) ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 Å
AuthorsKennedy, A.E. / Pellegrini, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01GM133844-01 United States
CitationJournal: Structure / Year: 2025
Title: The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition.
Authors: Kennedy, A.E. / Barczewski, A.H. / Arnoldy, C.R. / Pennington, J.P. / Tiernan, K.A. / Hidalgo, M.B. / Reilly, C.C. / Wongsri, T. / Ragusa, M.J. / Grigoryan, G. / Mierke, D.F. / Pellegrini, M.
History
DepositionSep 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 16, 2025Group: 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: Engineered NEMO minimal IKK-binding domain
B: Engineered NEMO minimal IKK-binding domain
C: Engineered NEMO minimal IKK-binding domain
D: Engineered NEMO minimal IKK-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,64824
Polymers32,6404
Non-polymers3,00720
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Crosslinking experiments with different lengths of linkers produced mostly dimers with some tetramers and monomers.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-107 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.514, 40.892, 50.150
Angle α, β, γ (deg.)92.620, 106.140, 98.870
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Engineered NEMO minimal IKK-binding domain


Mass: 8160.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 8 types, 159 molecules

#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
#3: Chemical
ChemComp-9JE / pentane-1,5-diol


Mass: 104.148 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12O2
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Y
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-ER3 / ERBIUM (III) ION


Mass: 167.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Er
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.77 % / Description: irregular rectangular prism
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus Buffer System 4 pH 6.5 (MOPSO, bis-tris), Morpheus Precipitant Mix (1,5-pentanediol, PEG 8000), lanthanides mix (erbium (III) chloride hexahydrate, terbium (III) chloride ...Details: Morpheus Buffer System 4 pH 6.5 (MOPSO, bis-tris), Morpheus Precipitant Mix (1,5-pentanediol, PEG 8000), lanthanides mix (erbium (III) chloride hexahydrate, terbium (III) chloride hexahydrate, ytterbium (III) chloride hexahydrate, yttrium (III) chloride hexahydrate), L-proline

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream (LN2) / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2022
RadiationMonochromator: horizontal bounce Si(111) double crysta / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.44→47.96 Å / Num. obs: 31670 / % possible obs: 91.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 13.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.086 / Net I/σ(I): 7.6
Reflection shellResolution: 1.44→1.61 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1584 / CC1/2: 0.426 / % possible all: 58

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot9.7model building
autoPROCdata reduction
STARANISOdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→40.23 Å / SU ML: 0.1203 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.6643
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.202 2000 6.32 %
Rwork0.1727 29669 -
obs0.1746 31669 61.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.47 Å2
Refinement stepCycle: LAST / Resolution: 1.44→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 150 139 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172407
X-RAY DIFFRACTIONf_angle_d1.50263199
X-RAY DIFFRACTIONf_chiral_restr0.0777314
X-RAY DIFFRACTIONf_plane_restr0.0119422
X-RAY DIFFRACTIONf_dihedral_angle_d18.98951026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.470.701130.327145X-RAY DIFFRACTION1.31
1.47-1.510.3617130.2452189X-RAY DIFFRACTION5.48
1.51-1.560.3205280.2578402X-RAY DIFFRACTION11.79
1.56-1.610.3504480.2559719X-RAY DIFFRACTION21.05
1.61-1.660.2732780.22811167X-RAY DIFFRACTION33.91
1.66-1.730.26241080.22271605X-RAY DIFFRACTION46.61
1.73-1.810.2521470.21882172X-RAY DIFFRACTION63.08
1.81-1.90.25371900.20792829X-RAY DIFFRACTION82.58
1.91-2.020.20932260.19573350X-RAY DIFFRACTION97.44
2.02-2.180.19852330.16533447X-RAY DIFFRACTION99.97
2.18-2.40.18912320.14663436X-RAY DIFFRACTION99.89
2.4-2.750.19022310.15713434X-RAY DIFFRACTION100
2.75-3.460.18062320.16093437X-RAY DIFFRACTION99.97
3.46-40.230.19142310.16933437X-RAY DIFFRACTION99.81

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