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- PDB-2zvo: NEMO CoZi domain in complex with diubiquitin in C2 space group -

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Basic information

Entry
Database: PDB / ID: 2zvo
TitleNEMO CoZi domain in complex with diubiquitin in C2 space group
Components
  • NF-kappa-B essential modulator
  • UBC protein
KeywordsTranscription/SIGNALING PROTEIN / NF-kB signaling / Ubiquitin binding / Coiled coil / Cytoplasm / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / Transcription-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


SLC15A4:TASL-dependent IRF5 activation / Modulation of host responses by IFN-stimulated genes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / Regulation of NF-kappa B signaling / TNFR1-induced NF-kappa-B signaling pathway / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling ...SLC15A4:TASL-dependent IRF5 activation / Modulation of host responses by IFN-stimulated genes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / Regulation of NF-kappa B signaling / TNFR1-induced NF-kappa-B signaling pathway / 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 / IKK complex recruitment mediated by RIP1 / establishment of vesicle localization / linear polyubiquitin binding / PKR-mediated signaling / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / 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 / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / B cell homeostasis / positive regulation of macroautophagy / Maturation of protein E / Maturation of protein E / canonical NF-kappaB signal transduction / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / ubiquitin ligase complex / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation
Similarity search - Function
Nemo cc2-lz domain - 1d5 darpin complex / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Nemo cc2-lz domain - 1d5 darpin complex / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NF-kappa-B essential modulator / Polyubiquitin-C / UBC protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 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 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBC protein
G: UBC protein
B: NF-kappa-B essential modulator
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)55,9124
Polymers55,9124
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-61 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.861, 98.372, 50.616
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UBC protein


Mass: 17279.785 Da / Num. of mol.: 2 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q96C32, UniProt: P0CG48*PLUS
#2: 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: 10676.148 Da / Num. of mol.: 2 / Fragment: CC2-LZ, CoZi domain / Mutation: E282A, K285A
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): BL21 / References: UniProt: O88522
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.85 Å3/Da / Density % sol: 56.84 % / Mosaicity: 0.727 °
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 17, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15653 / % possible obs: 88.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.162 / Χ2: 1.522 / Net I/σ(I): 6.462
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.81.60.2369310.73553
2.8-2.911.80.22711740.98367.5
2.91-3.0420.22214111.16480.1
3.04-3.22.30.24316021.00391
3.2-3.42.80.23817161.12398.6
3.4-3.663.20.27917402.7299.3
3.66-4.033.40.24517452.82499.8
4.03-4.623.50.1517671.06499.9
4.62-5.813.40.12517711.01599.9
5.81-503.50.09717961.07899.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
MOLREPphasing
RefinementResolution: 2.9→49.2 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.759 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27699 646 5.1 %RANDOM
Rwork0.2374 ---
obs0.23956 11951 89.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.41 Å2 / Biso mean: 49.856 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.48 Å20 Å2-2.57 Å2
2--1.09 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 0 174 3969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9925149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.78826.296189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64915800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1491521
X-RAY DIFFRACTIONr_chiral_restr0.1580.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022801
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.21931
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22610
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.52417
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95823800
X-RAY DIFFRACTIONr_scbond_it1.1231530
X-RAY DIFFRACTIONr_scangle_it1.8274.51349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 29 -
Rwork0.298 760 -
all-789 -
obs--74.57 %

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