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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) / SLC15A4:TASL-dependent IRF5 activation / protein linear polyubiquitination / IkappaB kinase complex / 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) / SLC15A4:TASL-dependent IRF5 activation / protein linear polyubiquitination / IkappaB kinase complex / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / 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 / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Regulation of TNFR1 signaling / ubiquitin binding / Activation of NF-kappaB in B cells / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / CLEC7A (Dectin-1) signaling / positive regulation of NF-kappaB transcription factor activity / FCERI mediated NF-kB activation / PKR-mediated signaling / Interleukin-1 signaling / response to virus / cytoplasmic side of plasma membrane / Ovarian tumor domain proteases / protein polyubiquitination / spindle pole / ubiquitin-protein transferase activity / mitotic spindle / Downstream TCR signaling / ubiquitin protein ligase activity / ER-Phagosome pathway / T cell receptor signaling pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / defense response to bacterium / immune response / inflammatory response / protein heterodimerization activity / protein domain specific binding / innate immune response / ubiquitin protein ligase binding / apoptotic process / DNA damage response / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / NEMO, Zinc finger / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / NEMO, Zinc finger / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tail fiber / 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
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Has protein modificationY

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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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