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- PDB-6yek: Crystal structure of human NEMO apo form -

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Basic information

Entry
Database: PDB / ID: 6yek
TitleCrystal structure of human NEMO apo form
ComponentsInhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b
KeywordsPROTEIN BINDING / Cell signaling / NF-kB pathway
Function / homology
Function and homology information


IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / signaling adaptor activity / canonical NF-kappaB signal transduction / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / Downstream TCR signaling / kinase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / phosphorylation / defense response to bacterium / inflammatory response / immune response / protein heterodimerization activity / protein domain specific binding / innate immune response / ubiquitin protein ligase binding / apoptotic process / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
Similarity search - Domain/homology
Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGarcia-Pardo, J. / Akutsu, M. / Busse, P. / Skenderovic, A. / Maculins, T. / Dikic, I.
CitationJournal: Cell Chem Biol / Year: 2020
Title: Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms.
Authors: Maculins, T. / Garcia-Pardo, J. / Skenderovic, A. / Gebel, J. / Putyrski, M. / Vorobyov, A. / Busse, P. / Varga, G. / Kuzikov, M. / Zaliani, A. / Rahighi, S. / Schaeffer, V. / Parnham, M.J. ...Authors: Maculins, T. / Garcia-Pardo, J. / Skenderovic, A. / Gebel, J. / Putyrski, M. / Vorobyov, A. / Busse, P. / Varga, G. / Kuzikov, M. / Zaliani, A. / Rahighi, S. / Schaeffer, V. / Parnham, M.J. / Sidhu, S.S. / Ernst, A. / Dotsch, V. / Akutsu, M. / Dikic, I.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b
B: Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b


Theoretical massNumber of molelcules
Total (without water)20,6642
Polymers20,6642
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.760, 85.760, 99.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c

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Components

#1: Protein Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b


Mass: 10331.796 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, hCG_2003089 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DWY0, UniProt: Q9Y6K9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 4.4 Å3/Da / Density % sol: 72.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 45% (v/v) ethylene glycol 50mM acetate (pH 4.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→85.79 Å / Num. obs: 6469 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 35.8
Reflection shellResolution: 3.2→3.32 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 8.2 / Num. unique obs: 638 / CC1/2: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F89

3f89


Resolution: 3.2→85.76 Å / SU ML: 0.6075 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.569
RfactorNum. reflection% reflection
Rfree0.3359 646 9.99 %
Rwork0.2909 --
obs0.2954 6464 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→85.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 0 45 1427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01371390
X-RAY DIFFRACTIONf_angle_d1.85911858
X-RAY DIFFRACTIONf_chiral_restr0.0879210
X-RAY DIFFRACTIONf_plane_restr0.0119246
X-RAY DIFFRACTIONf_dihedral_angle_d20.3265177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.47691250.4231122X-RAY DIFFRACTION99.84
3.45-3.80.40871250.35271138X-RAY DIFFRACTION99.84
3.8-4.350.37341280.29961151X-RAY DIFFRACTION99.84
4.35-5.480.35991300.29421166X-RAY DIFFRACTION99.77
5.48-85.760.26121380.24511241X-RAY DIFFRACTION98.92

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