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- PDB-6xx0: Crystal structure of NEMO in complex with Ubv-LIN -

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Basic information

Entry
Database: PDB / ID: 6xx0
TitleCrystal structure of NEMO in complex with Ubv-LIN
Components
  • Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b
  • Ubv-LIN
KeywordsPROTEIN BINDING / Inhibitor / Ubiquitin
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 / SLC15A4:TASL-dependent IRF5 activation / 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 ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / SLC15A4:TASL-dependent IRF5 activation / 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 / canonical NF-kappaB signal transduction / ubiquitin ligase complex / signaling adaptor activity / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / spindle pole / FCERI mediated NF-kB activation / 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 / defense response to bacterium / inflammatory response / immune response / protein heterodimerization activity / protein domain specific binding / innate immune response / ubiquitin protein ligase binding / DNA damage response / apoptotic process / 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 / cytosol / cytoplasm
Similarity search - Function
NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / 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: 2.6 Å
AuthorsAkutsu, M. / Skenderovic, A. / Garcia-Pardo, J. / 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
DepositionJan 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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:
MolmilJmol/JSmol

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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
C: Ubv-LIN
D: Ubv-LIN


Theoretical massNumber of molelcules
Total (without water)38,5624
Polymers38,5624
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-71 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.323, 80.773, 84.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 phage EcSzw-2 (virus) / References: UniProt: D3DWY0, UniProt: Q9Y6K9*PLUS
#2: Protein Ubv-LIN


Mass: 8949.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia phage EcSzw-2 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22.5% polyethylene glycol 3350, 0.1M Magnesium chloride, 0.1M Try-HCl, pH 7.0

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→44.99 Å / Num. obs: 101221 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 2213 / CC1/2: 0.548

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f89

3f89


Resolution: 2.6→40.42 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.093 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.333
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 1587 10.3 %RANDOM
Rwork0.2384 ---
obs0.2437 13833 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.01 Å2 / Biso mean: 53.685 Å2 / Biso min: 16.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20 Å2
2--1.81 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.6→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 0 88 2503
Biso mean---44.2 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132438
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172340
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.6493277
X-RAY DIFFRACTIONr_angle_other_deg1.1241.5815477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0675298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85925.515136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14515494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5111511
X-RAY DIFFRACTIONr_chiral_restr0.0480.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022674
X-RAY DIFFRACTIONr_gen_planes_other00.02415
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 110 -
Rwork0.305 997 -
all-1107 -
obs--100 %

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