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- PDB-7tv4: Crystal structure of NEMO CoZi in complex with HOIP NZF1 and line... -

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Basic information

Entry
Database: PDB / ID: 7tv4
TitleCrystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin
Components
  • E3 ubiquitin-protein ligase RNF31
  • NF-kappa-B essential modulator
  • Polyubiquitin-C
KeywordsSIGNALING PROTEIN / Ubiquitin signaling / NF-kappa B signaling
Function / homology
Function and homology information


IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / protein linear polyubiquitination / IkappaB kinase complex / SLC15A4:TASL-dependent IRF5 activation / LUBAC complex / establishment of vesicle localization / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / protein linear polyubiquitination / IkappaB kinase complex / SLC15A4:TASL-dependent IRF5 activation / LUBAC complex / establishment of vesicle localization / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / transferrin receptor binding / positive regulation of xenophagy / IkBA variant leads to EDA-ID / CD40 receptor complex / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / negative regulation of necroptotic process / positive regulation of ubiquitin-dependent protein catabolic process / anoikis / Modulation of host responses by IFN-stimulated genes / 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 / TRAF6 mediated NF-kB activation / B cell homeostasis / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Maturation of protein E / Maturation of protein E / signaling adaptor activity / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / ubiquitin binding / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation
Similarity search - Function
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 / : / : / : / : ...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. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase RNF31 / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsRahighi, S. / Iyer, M. / Oveisi, H.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Sci Rep / Year: 2022
Title: Structural basis for the simultaneous recognition of NEMO and acceptor ubiquitin by the HOIP NZF1 domain.
Authors: Rahighi, S. / Iyer, M. / Oveisi, H. / Nasser, S. / Duong, V.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NF-kappa-B essential modulator
C: Polyubiquitin-C
D: NF-kappa-B essential modulator
G: Polyubiquitin-C
K: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2296
Polymers61,1645
Non-polymers651
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.950, 69.560, 180.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 11293.829 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K9
#2: Protein Polyubiquitin-C


Mass: 17423.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Protein/peptide E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 3728.269 Da / Num. of mol.: 1 / Fragment: Residues 350-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, 22% v/v PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→56.01 Å / Num. obs: 5542 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.83 / Χ2: 1 / Net I/σ(I): 9.5
Reflection shellResolution: 4.2→4.7 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1543 / CC1/2: 0.42 / Χ2: 0.93 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4owf

4owf


Resolution: 4.2→56.01 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.855 / SU B: 70.419 / SU ML: 0.844 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 285 5.2 %RANDOM
Rwork0.2221 ---
obs0.2254 5239 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.88 Å2 / Biso mean: 90.975 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--6.49 Å20 Å2
3----7.78 Å2
Refinement stepCycle: final / Resolution: 4.2→56.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 1 11 3906
Biso mean--87.09 35.55 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133934
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173848
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.6525284
X-RAY DIFFRACTIONr_angle_other_deg1.1181.5858988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4245481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.90224.558215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.52215817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6131523
X-RAY DIFFRACTIONr_chiral_restr0.0550.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024275
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02682
LS refinement shellResolution: 4.2→4.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 20 -
Rwork0.296 391 -
all-411 -
obs--100 %

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