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- PDB-4owf: Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain -

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Basic information

Entry
Database: PDB / ID: 4owf
TitleCrystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
Components
  • E3 ubiquitin-protein ligase RNF31
  • NF-kappa-B essential modulator
KeywordsTRANSCRIPTION/PROTEIN BINDING / LUBAC / NF-kappa B / NEMO / HOIP / TRANSCRIPTION-PROTEIN BINDING 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / protein linear polyubiquitination / IkappaB kinase complex / Regulation of TNFR1 signaling / TRAF6 mediated NF-kB activation / LUBAC complex / 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 / RBR-type E3 ubiquitin transferase / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / CD40 signaling pathway / Downstream TCR signaling / transferrin receptor binding / positive regulation of xenophagy / activated TAK1 mediates p38 MAPK activation / CD40 receptor complex / NOD1/2 Signaling Pathway / Ub-specific processing proteases / negative regulation of necroptotic process / anoikis / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / B cell homeostasis / positive regulation of macroautophagy / canonical NF-kappaB signal transduction / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / signaling adaptor activity / ubiquitin binding / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of NF-kappaB transcription factor activity / cytoplasmic side of plasma membrane / protein polyubiquitination / spindle pole / ubiquitin-protein transferase activity / mitotic spindle / ubiquitin protein ligase activity / T cell receptor signaling pathway / 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 / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nemo cc2-lz domain - 1d5 darpin complex / E3 ubiquitin-protein ligase RNF31, UBA domain / NF-kappa-B essential modulator NEMO, N-terminal / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : ...Nemo cc2-lz domain - 1d5 darpin complex / E3 ubiquitin-protein ligase RNF31, UBA domain / NF-kappa-B essential modulator NEMO, N-terminal / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / : / NF-kappa-B essential modulator NEMO / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / C2H2 type zinc-finger / PNGase/UBA- or UBX-containing domain / 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 / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NF-kappa-B essential modulator / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRahighi, S. / Fujita, H. / Kawasaki, M. / Kato, R. / Iwai, K. / Wakatsuki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Mol.Cell.Biol. / Year: 2014
Title: Mechanism Underlying I kappa B Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex.
Authors: Fujita, H. / Rahighi, S. / Akita, M. / Kato, R. / Sasaki, Y. / Wakatsuki, S. / Iwai, K.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Other
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Mar 16, 2016Group: Source and taxonomy
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.6Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: NF-kappa-B essential modulator
B: NF-kappa-B essential modulator
G: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6794
Polymers24,6133
Non-polymers651
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-59 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.410, 81.410, 74.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 10648.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ikbkg,Nemo / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O88522, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin- ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 3316.815 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31,ZIBRA / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.92 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Co-crystals were obtained after 6 days in 20% (w/v) PEG-3350 and 0.2 M DL-malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.28254 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28254 Å / Relative weight: 1
ReflectionResolution: 2→32.96 Å / Num. all: 120482 / Num. obs: 15849 / % possible obs: 83.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.1 / % possible all: 66.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY . 3FX0 AND 2WX0

3fx0

2wx0


Resolution: 2→32.96 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.846 / SU B: 4.726 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31267 974 5.1 %RANDOM
Rwork0.25893 ---
obs0.26152 17945 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.55 Å20 Å2
2--0.55 Å20 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 2→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 1 100 1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191657
X-RAY DIFFRACTIONr_bond_other_d0.0050.021651
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9732216
X-RAY DIFFRACTIONr_angle_other_deg0.84433802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8585195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54126.08297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98815350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 83 -
Rwork0.281 1307 -
obs--99.14 %

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