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- PDB-9azj: Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 -

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Basic information

Entry
Database: PDB / ID: 9azj
TitleStructure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1
Components
  • E3 ubiquitin-protein ligase RNF31
  • NF-kappa-B essential modulator
  • Ubiquitin
KeywordsSIGNALING PROTEIN / ubiquitin binding domain / UBAN / NZF / NF-kB / NEMO
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 / protein linear polyubiquitination / LUBAC complex / establishment of vesicle localization / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / transferrin receptor binding ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / protein linear polyubiquitination / LUBAC complex / establishment of vesicle localization / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / 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 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / negative regulation of necroptotic process / anoikis / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked polyubiquitin modification-dependent protein binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / positive regulation of T cell receptor signaling pathway / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / Regulation of pyruvate metabolism / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / signaling adaptor activity / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential
Similarity search - Function
: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair ...: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / C2H2 type zinc-finger / PNGase/UBA- or UBX-containing domain / 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 / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger 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 signature. / Zinc finger, RanBP2-type superfamily / 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-B / E3 ubiquitin-protein ligase RNF31 / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsMichel, M.A. / Scutts, S. / Komander, D.
Funding support United Kingdom, Australia, European Union, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192732 United Kingdom
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
European Research Council (ERC)724804European Union
CitationJournal: To be published
Title: Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin
Authors: Michel, M.A. / Scutts, S. / Komander, D.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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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
C: NF-kappa-B essential modulator
D: NF-kappa-B essential modulator
E: E3 ubiquitin-protein ligase RNF31
F: Ubiquitin
G: E3 ubiquitin-protein ligase RNF31
S: Ubiquitin
Z: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,06511
Polymers82,9349
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.828, 101.447, 144.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: 12643.395 Da / Num. of mol.: 4 / Mutation: K285C
Source method: isolated from a genetically manipulated source
Details: K285C mutation for chemical ubiquitination / Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K9
#2: 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: 3245.738 Da / Num. of mol.: 2 / Fragment: HOIP NZF domain, residues 351-379
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
#3: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 3 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.6
Details: 150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.32→55.81 Å / Num. obs: 15095 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 122.12 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.048 / Rrim(I) all: 0.115 / Net I/σ(I): 9.1 / Num. measured all: 84793
Reflection shellResolution: 3.32→3.59 Å / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.077 / Num. measured all: 17542 / Num. unique obs: 3039 / CC1/2: 0.688 / Rpim(I) all: 0.475 / Rrim(I) all: 1.18 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→50.72 Å / SU ML: 0.4796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: poorly ordered ubiquitin and HOIP NZF domain (chain E, F). NEMO chain A and chain B chemically ubiquitinated via a disulphide bond at NEMO K285C-Ub G76C.
RfactorNum. reflection% reflection
Rfree0.2847 729 4.85 %
Rwork0.2408 14297 -
obs0.2431 15026 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 167.35 Å2
Refinement stepCycle: LAST / Resolution: 3.32→50.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 2 0 4258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174294
X-RAY DIFFRACTIONf_angle_d0.44335829
X-RAY DIFFRACTIONf_chiral_restr0.035722
X-RAY DIFFRACTIONf_plane_restr0.0024762
X-RAY DIFFRACTIONf_dihedral_angle_d12.82141517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.580.3981340.32752824X-RAY DIFFRACTION99.73
3.58-3.940.37831500.27582806X-RAY DIFFRACTION99.8
3.94-4.510.2781540.22442828X-RAY DIFFRACTION100
4.51-5.680.24771320.2442858X-RAY DIFFRACTION99.6
5.68-50.720.26711590.2242981X-RAY DIFFRACTION99.49
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.797011882191.83575271286-2.261145789627.21509303321-3.682458798134.1191126409-0.1223330873940.232886617434-0.18029584090.6393758206890.106403956922-0.903934690095-0.650744415569-0.7405815481950.1632705550040.4640559480920.0287014416437-0.08584965183590.9133407076460.1075599180660.6069715110363.0455988113926.5659494323-7.57797698195
22.219094383650.748988575661-1.213766496614.61002983315-3.224880776125.976670965280.2392339286210.0721228993818-0.0663416492121-0.382292025310.09965200292020.6677071928310.448437425368-0.0929606630226-0.2589788059220.3086800610910.0511998121149-0.02342490322930.6711154709320.08568903609220.4499530306791.8665298575525.0193103401-6.58588238909
32.169980076971.862258390012.186192621979.63806340852-2.077585799683.740459060160.1881683386310.573143923334-0.215216629395-0.7892412864710.212149558673-0.7885902886150.4804825934740.3837199137880.04842908024660.3789395949240.0484212626862-0.0931955128050.569336855188-0.04033703545070.485720304083-11.136771118522.573061891-14.4640662394
41.40479538261-0.818229887130.1548764946350.219248021949-0.2351342592983.894529880660.2633276843070.1815429141760.135506217062-0.00258492047684-0.5438691045820.4195954950520.295766312238-0.146313916656-0.1014888468150.7206700347150.08535118090660.1248316189630.579297138593-0.04654199842540.781622646146-14.250620771525.8974682261-14.5363466749
51.628858004762.514047053281.21274682984.400706569981.937425253280.9027836816293.49528014902-4.302795500753.494096972631.35216373986-0.7801939983690.404728925009-1.11256712031.254588226940.009126481085474.58087304334-1.887273794631.289401711453.44338504484-1.361826510913.74038768264-21.0820650512-21.2700471806-18.0555003106
65.34828977932-3.64705904349-2.335215491344.53937326041-2.161970762588.918901055750.319065479647-1.616588159792.0426737209-0.4263568589930.3463075448862.388835485360.503992021968-5.04988946261-1.060189043892.86228779782-0.928975597016-0.03966613151793.87418221539-0.98757385113.42919813011-37.5763912886-10.6243839339-18.0199427415
74.26586905677-2.550734571154.31362518363.35816851396-2.478250753195.123342592690.58579606137-1.01248700671-1.450307945110.598347314613-1.977249624930.9391135721561.424683005480.02171749293091.38819608591.03075979746-0.2160974530730.2131476343020.9040515705590.2233227252241.37066050107-14.5859911526-6.5358360522218.0586629087
85.55012812718-0.8697991923983.5873221444.085545300521.396223227655.462737242480.0996847928267-1.280904066080.3469560385010.598727096972-0.11184009720.801321454412-0.256916275318-1.51472567479-0.3404646373690.6465707934070.1120642671390.1335553899850.971224609799-0.0648023453430.8587131119932.4927398179928.356966718613.6439101615
98.66889172244-5.4392319369-0.5993367368686.886391977310.4556012415697.277008065870.7479187960681.67812586329-0.784998020139-0.783644708566-0.9108557490790.8359695829490.517654628885-0.2577678657030.110719195950.888131647682-0.193380192043-0.04826621388871.53867362987-0.1625788857760.706851901911-25.9265636377-0.6724211835974.31494838072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 259 through 343)AA259 - 3431 - 85
22(chain 'B' and resid 260 through 342)BB260 - 3421 - 83
33(chain 'C' and resid 265 through 337)CC265 - 3371 - 73
44(chain 'D' and resid 269 through 339)DD269 - 3391 - 71
55(chain 'E' and resid 353 through 379)EE353 - 3791 - 27
66(chain 'F' and resid 1 through 71)FF1 - 711 - 71
77(chain 'G' and resid 353 through 379)GG353 - 3791 - 27
88(chain 'S' and resid 1 through 76)SJ1 - 761 - 76
99(chain 'Z' and resid 1 through 76)ZK1 - 761 - 76

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