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- PDB-3f89: NEMO CoZi domain -

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Basic information

Entry
Database: PDB / ID: 3f89
TitleNEMO CoZi domain
ComponentsNF-kappa-B essential modulator
KeywordsTRANSCRIPTION / NF-kB signaling / Ubiquitin binding / Coiled coil / Cytoplasm / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger
Function / homology
Function and homology information


IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IkappaB kinase complex / TRAF6 mediated NF-kB activation / Ovarian tumor domain proteases / PKR-mediated signaling / establishment of vesicle localization / linear polyubiquitin binding / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / transferrin receptor binding / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Ub-specific processing proteases / anoikis / peroxisome proliferator activated receptor binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / B cell homeostasis / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / signaling adaptor activity / ubiquitin ligase complex / tumor necrosis factor-mediated signaling pathway / mitotic spindle / spindle pole / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / protein heterodimerization activity / protein domain specific binding / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nemo cc2-lz domain - 1d5 darpin complex / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NF-kappa-B essential modulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsRahighi, S. / Ikeda, F. / Kawasaki, M. / Akutsu, M. / Suzuki, N. / Kato, R. / Kensche, T. / Uejima, T. / Bloor, S. / Komander, D. ...Rahighi, S. / Ikeda, F. / Kawasaki, M. / Akutsu, M. / Suzuki, N. / Kato, R. / Kensche, T. / Uejima, T. / Bloor, S. / Komander, D. / Randow, F. / Wakatsuki, S. / Dikic, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation
Authors: Rahighi, S. / Ikeda, F. / Kawasaki, M. / Akutsu, M. / Suzuki, N. / Kato, R. / Kensche, T. / Uejima, T. / Bloor, S. / Komander, D. / Randow, F. / Wakatsuki, S. / Dikic, I.
History
DepositionNov 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NF-kappa-B essential modulator
B: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)21,5542
Polymers21,5542
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-50 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.088, 85.088, 101.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein NF-kappa-B essential modulator / NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / ...NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / I-kappa-B kinase gamma / IKK-gamma / IKKG / IkB kinase-associated protein 1 / IKKAP1 / mFIP-3


Mass: 10777.210 Da / Num. of mol.: 2 / Fragment: CC2-LZ, CoZi domain / Mutation: K285N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O88522
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 4.25 Å3/Da / Density % sol: 71.05 % / Mosaicity: 0.802 °
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 14 % / Number: 151051 / Rmerge(I) obs: 0.093 / Χ2: 1.1 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 10752 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.810.050.97812.6
4.625.8110010.0531.04113.8
4.034.6210010.0510.99514
3.664.0310010.0711.06414.2
3.43.6610010.1061.05214.3
3.23.410010.1871.09214.3
3.043.210010.2691.13514.4
2.913.0410010.3291.17314.3
2.82.9110010.4341.21514.4
2.72.810010.6281.22514.4
ReflectionResolution: 2.8→50 Å / Num. all: 9693 / Num. obs: 9684 / Redundancy: 14 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 7.2 / Num. unique all: 929

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.46 Å / D res low: 50 Å / FOM : 0.28 / Reflection: 5147
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.3120.610.0780.969
2Se600.3270.6550.0610.672
Phasing MAD shell
Resolution (Å)FOM Reflection
12.38-500.27283
7.83-12.380.32450
6.13-7.830.38549
5.2-6.130.3638
4.6-5.20.29715
4.16-4.60.27769
3.83-4.160.25844
3.57-3.830.23899

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.8→42.54 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.83 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.314 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.53 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31 466 4.8 %RANDOM
Rwork0.284 ---
obs0.285 9659 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.97 Å2 / Biso mean: 51.408 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 0 69 1453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221397
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9791868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26626.66784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.01315303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.099158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021044
X-RAY DIFFRACTIONr_nbd_refined0.2520.2713
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3880.28
X-RAY DIFFRACTIONr_mcbond_it0.6451.5844
X-RAY DIFFRACTIONr_mcangle_it1.18821322
X-RAY DIFFRACTIONr_scbond_it1.163591
X-RAY DIFFRACTIONr_scangle_it2.0384.5546
LS refinement shellResolution: 2.798→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 35 -
Rwork0.397 660 -
all-695 -
obs--99 %

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