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- PDB-9avt: Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 9avt
TitleStructure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin
Components
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
  • Ubiquitin
KeywordsSIGNALING PROTEIN / ubiquitin binding domain / diubiquitin / Lys6-linkage / mitophagy
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / positive regulation of protein kinase activity / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / K63-linked polyubiquitin modification-dependent protein binding / non-canonical NF-kappaB signal transduction / seminiferous tubule development / female gonad development ...hypothalamus gonadotrophin-releasing hormone neuron development / positive regulation of protein kinase activity / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / K63-linked polyubiquitin modification-dependent protein binding / non-canonical NF-kappaB signal transduction / seminiferous tubule development / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Nuclear signaling by ERBB4 / neuron projection morphogenesis / energy homeostasis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / 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 / regulation of neuron apoptotic process / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / negative regulation of autophagy / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / Regulation of activated PAK-2p34 by proteasome mediated degradation / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / Regulation of NF-kappa B signaling / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Stabilization of p53
Similarity search - Function
TAB2/3, CUE domain / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type ...TAB2/3, CUE domain / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Polyubiquitin-B / TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 4, 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2699
Polymers20,6653
Non-polymers6046
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.323, 90.323, 86.335
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Components on special symmetry positions
IDModelComponents
11A-100-

SO4

21B-241-

HOH

31C-803-

HOH

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
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
#2: Protein/peptide TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 2 / TAK1-binding protein 2 / ...Mitogen-activated protein kinase kinase kinase 7-interacting protein 2 / TAK1-binding protein 2 / TAB-2 / TGF-beta-activated kinase 1-binding protein 2


Mass: 3511.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAB2, KIAA0733, MAP3K7IP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYJ8

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Non-polymers , 4 types, 139 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsLys6-linkage between molecules A and B, not resolved in crystal structure
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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.5→45.16 Å / Num. obs: 33838 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 20 / Num. measured all: 217524
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 1.028 / Num. measured all: 10260 / Num. unique obs: 1646 / CC1/2: 0.636 / Rpim(I) all: 0.445 / Rrim(I) all: 1.123 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.02 Å / SU ML: 0.1826 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2033 1707 5.05 %
Rwork0.1824 32086 -
obs0.1835 33793 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.91 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 29 133 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01261459
X-RAY DIFFRACTIONf_angle_d1.35061983
X-RAY DIFFRACTIONf_chiral_restr0.0942235
X-RAY DIFFRACTIONf_plane_restr0.0103252
X-RAY DIFFRACTIONf_dihedral_angle_d19.9565568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.35451320.32182629X-RAY DIFFRACTION99.75
1.54-1.590.30731280.26132626X-RAY DIFFRACTION99.93
1.59-1.650.28991250.21812641X-RAY DIFFRACTION99.93
1.65-1.720.23481500.1992610X-RAY DIFFRACTION99.89
1.72-1.80.19981140.19842650X-RAY DIFFRACTION99.93
1.8-1.890.25311640.19982637X-RAY DIFFRACTION99.96
1.89-2.010.20631530.18882649X-RAY DIFFRACTION99.96
2.01-2.160.2061270.17822658X-RAY DIFFRACTION99.93
2.16-2.380.22071560.18232671X-RAY DIFFRACTION100
2.38-2.730.23011430.18522690X-RAY DIFFRACTION99.96
2.73-3.430.22531440.18822740X-RAY DIFFRACTION99.97
3.44-40.020.15541710.16012885X-RAY DIFFRACTION99.97
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)
12.89781708969-0.680812771787-0.4711598247273.85557336474-1.267510158823.007314521870.001672456744760.221234769510.0197340779852-0.303867806975-0.164249946753-0.3600743950420.0566785520710.0698014788540.1495764080340.2561123581320.009097675934950.04371281761980.160748870185-0.0021174919740.23752901150656.2822949597-5.46014719587-10.8824791264
25.559875540810.6500921193140.402858194516.61887718850.4781367381064.54226614214-0.08109556487590.1259828131960.149655996693-0.01882867149160.0631572187128-0.0422184092070.0599757091563-0.0837929137125-0.01093166475780.157232080171-0.0254926019605-0.01883411731040.158175049776-0.004280216329480.14895375772831.8441430164-19.6046424053-8.91779592952
37.163835618460.625141779902-0.12159001428.00653382945-0.1459900291124.950532986380.0961607779275-0.560993318336-0.3826223284340.257076230641-0.0821991051450.03354340920770.126483445528-0.008300790909750.02996089914550.182617833558-0.0261545284675-0.006891033433170.1503181643870.0174632799450.12660441792141.907218126-8.974747338052.69805448363
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 1 through 73)AA1 - 731 - 73
22(chain 'B' and resid 1 through 73)BB1 - 731 - 73
33(chain 'C' and resid 664 through 693)CC664 - 6931 - 30

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