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

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Basic information

Entry
Database: PDB / ID: 9avw
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 / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / non-canonical NF-kappaB signal transduction ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / non-canonical NF-kappaB signal transduction / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / positive regulation of protein kinase activity / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Nuclear signaling by ERBB4 / 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 / negative regulation of autophagy / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
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 signature. / Zinc finger, RanBP2-type superfamily / 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 signature. / Zinc finger, RanBP2-type superfamily / 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
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: 1.747 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 5, 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)38,69910
Polymers38,0573
Non-polymers6427
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.663, 89.663, 86.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31B-101-

SO4

41A-355-

HOH

51C-805-

HOH

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Components

#1: Protein Ubiquitin


Mass: 17215.633 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: 3626.109 Da / Num. of mol.: 1 / Fragment: NZF domain, residues 663 to 693
Source method: isolated from a genetically manipulated source
Details: = / Source: (gene. exp.) Homo sapiens (human) / Gene: TAB2, KIAA0733, MAP3K7IP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYJ8
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 121 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.2 M ammonium sulphate, 20% glycerol / Temp details: room temperature

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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 PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.747→44.831 Å / Num. obs: 21100 / % possible obs: 99.2 % / Redundancy: 18.6 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.089 / Net I/σ(I): 7.2
Reflection shellResolution: 1.747→1.839 Å / Redundancy: 16.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2714 / CC1/2: 0.523 / Rpim(I) all: 0.248 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.747→44.831 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1006 4.77 %5%
Rwork0.1935 ---
obs0.1948 21100 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.747→44.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 31 121 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061455
X-RAY DIFFRACTIONf_angle_d0.881977
X-RAY DIFFRACTIONf_dihedral_angle_d7.9151185
X-RAY DIFFRACTIONf_chiral_restr0.059228
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.747-1.83890.38031360.31892714X-RAY DIFFRACTION96
1.8389-1.95410.25711420.25482813X-RAY DIFFRACTION99
1.9541-2.1050.23921360.20992834X-RAY DIFFRACTION99
2.105-2.31680.20711550.19062826X-RAY DIFFRACTION99
2.3168-2.6520.20591290.18182896X-RAY DIFFRACTION100
2.652-3.34110.20411490.1852919X-RAY DIFFRACTION100
3.3411-44.8310.20671590.16693092X-RAY DIFFRACTION100
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)
12.83060.137-0.56895.4726-3.30626.631-0.06080.10910.02240.1288-0.2361-0.5691-0.40130.5110.24840.2066-0.0093-0.02920.14650.02590.224961.7014-5.0652-5.0743
22.7036-2.3283-0.18927.1401-0.84691.890.10580.1575-0.0546-0.5085-0.2697-0.50560.21010.13820.11970.27630.03060.09340.1277-0.00550.218759.2186-5.9236-16.4383
31.4317-2.206-1.96444.08992.72722.7918-0.32670.5155-0.6635-0.2261-0.22390.25060.5303-0.70150.1170.2967-0.04740.1284-0.1621-0.20850.24353.9486-13.9857-11.9491
43.57431.1182-4.75712.423-0.73646.74850.090.66170.0635-0.5980.11920.11690.1433-0.88210.10490.2970.05660.010.12660.00070.140148.3138-2.4056-12.7352
52.4442-0.4095-0.71296.101-1.83032.90710.15970.2020.18350.1414-0.10360.025-0.43760.09580.01390.2030.01660.02880.0745-0.00120.158853.6446-1.866-8.6754
65.5648-1.73331.33134.9856-0.64373.3519-0.12430.24990.0161-0.2310.0567-0.22180.21680.12620.07730.177-0.03270.03190.1721-0.02440.166335.1409-23.0791-10.8513
74.1226-0.4523-0.65051.8023-0.43933.59650.0548-0.1151-0.3495-0.05710.15660.00490.2542-0.3635-0.08020.1751-0.0978-0.01160.2282-0.07760.169226.9173-24.7501-8.8722
83.15970.66820.12594.4178-0.39694.4361-0.0798-0.01140.3685-0.1227-0.0320.1512-0.1286-0.47220.09060.1292-0.0253-0.01820.1501-0.03190.19230.719-15.4401-7.9248
94.1582-0.17541.19895.268-0.64152.8060.1328-0.35010.02130.361-0.00460.3602-0.0323-0.1898-0.08940.1436-0.00610.02560.0948-0.00810.071939.5054-4.54624.3976
104.80930.1664-0.70551.53230.14841.4255-0.06380.01240.02210.0050.0720.12580.0829-0.05680.01020.0983-0.00670.00380.0614-0.0110.096539.7191-8.12020.521
113.7738-0.1836-0.37024.19570.05755.4497-0.1538-0.9018-0.82720.3630.07930.14070.153-0.0431-0.05520.1290.02320.00730.19410.04590.112143.6699-12.49764.2636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 56 )
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 34 )
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 73 )
9X-RAY DIFFRACTION9chain 'C' and (resid 663 through 672 )
10X-RAY DIFFRACTION10chain 'C' and (resid 673 through 682 )
11X-RAY DIFFRACTION11chain 'C' and (resid 683 through 693 )

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