[English] 日本語
Yorodumi
- PDB-9avw: Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin -

+
Open data


ID or keywords:

Loading...

-
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 / non-canonical NF-kappaB signal transduction / mitochondrion transport along microtubule / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / non-canonical NF-kappaB signal transduction / mitochondrion transport along microtubule / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of protein kinase activity / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Nuclear signaling by ERBB4 / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / negative regulation of autophagy / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / PINK1-PRKN Mediated Mitophagy / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / ubiquitin binding / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / 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 / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / CUE domain / 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 / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / CUE domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more