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- PDB-7e62: Mouse TAB2 NZF in complex with Lys6-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 7.0E+62
TitleMouse TAB2 NZF in complex with Lys6-linked diubiquitin
Components
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
  • Ubiquitin
  • ubiquitin
KeywordsPROTEIN BINDING / UBIQUITIN
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex ...Formation of the ternary complex, and subsequently, the 43S complex / translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / Formation of a pool of free 40S subunits / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / SRP-dependent cotranslational protein targeting to membrane / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / Dual incision in TC-NER / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Asymmetric localization of PCP proteins
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 / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSato, Y. / Li, Y. / Okatsu, K. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05501 Japan
CitationJournal: Biophys.J. / Year: 2021
Title: Structural basis for specific recognition of K6-linked polyubiquitin chains by the TAB2 NZF domain.
Authors: Li, Y. / Okatsu, K. / Fukai, S. / Sato, Y.
History
DepositionFeb 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
H: ubiquitin
I: Ubiquitin
J: TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3539
Polymers46,9836
Non-polymers3693
Water86548
1
A: ubiquitin
B: Ubiquitin
C: TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7955
Polymers23,4923
Non-polymers3042
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: ubiquitin
I: Ubiquitin
J: TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5574
Polymers23,4923
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.694, 76.170, 114.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETVALVAL(chain 'A' and (resid 1 through 5 or resid 7 through 73))AA1 - 51 - 5
121THRTHRLEULEU(chain 'A' and (resid 1 through 5 or resid 7 through 73))AA7 - 737 - 73
231METMETVALVAL(chain 'B' and (resid 1 through 5 or resid 7 through 73))BB1 - 51 - 5
241THRTHRLEULEU(chain 'B' and (resid 1 through 5 or resid 7 through 73))BB7 - 737 - 73
351METMETVALVAL(chain 'H' and (resid 1 through 5 or resid 7 through 73))HD1 - 51 - 5
361THRTHRLEULEU(chain 'H' and (resid 1 through 5 or resid 7 through 73))HD7 - 737 - 73
471METMETVALVAL(chain 'I' and (resid 1 through 5 or resid 7 through 73))IE1 - 51 - 5
481THRTHRLEULEU(chain 'I' and (resid 1 through 5 or resid 7 through 73))IE7 - 737 - 73
192GLUGLUPHEPHEchain 'C'CC664 - 69326 - 55
2102GLUGLUPHEPHEchain 'J'JF664 - 69326 - 55

NCS ensembles :
ID
1
2

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Components

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Protein , 3 types, 6 molecules AHBICJ

#1: Protein ubiquitin


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K6R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps27a, Uba80, Ubcep1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62983
#2: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 2 / Mutation: A77D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps27a, Uba80, Ubcep1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62983
#3: Protein 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: 6194.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tab2, Kiaa0733, Map3k7ip2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99K90

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Non-polymers , 3 types, 51 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES-NaOH (pH 7.5), 1.44 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→42.46 Å / Num. obs: 28130 / % possible obs: 99.5 % / Redundancy: 13.2 % / Biso Wilson estimate: 37.95 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.11
Reflection shellResolution: 1.99→2.11 Å / Num. unique obs: 4318 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A9J

3a9j


Resolution: 1.99→42.46 Å / SU ML: 0.3129 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8551
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2636 1401 5 %
Rwork0.2419 26625 -
obs0.243 28026 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.04 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 17 48 2932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352920
X-RAY DIFFRACTIONf_angle_d0.86083934
X-RAY DIFFRACTIONf_chiral_restr0.0516455
X-RAY DIFFRACTIONf_plane_restr0.0043508
X-RAY DIFFRACTIONf_dihedral_angle_d25.51321143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.060.43411360.44772605X-RAY DIFFRACTION98.85
2.06-2.150.44911370.39872572X-RAY DIFFRACTION99.41
2.15-2.250.39351390.37652635X-RAY DIFFRACTION99.64
2.25-2.360.3611380.35082628X-RAY DIFFRACTION99.71
2.36-2.510.32851380.33732635X-RAY DIFFRACTION99.89
2.51-2.710.36551390.31532661X-RAY DIFFRACTION99.68
2.71-2.980.32751390.29532640X-RAY DIFFRACTION99.89
2.98-3.410.27071420.24812688X-RAY DIFFRACTION99.96
3.41-4.290.20171420.18392704X-RAY DIFFRACTION100
4.29-42.460.18581510.16072857X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.0561676031 Å / Origin y: -27.1027902164 Å / Origin z: -6.44422236983 Å
111213212223313233
T0.242069743813 Å20.0218559888498 Å20.00479935555318 Å2-0.744106819428 Å2-0.0344943228086 Å2--0.259512795868 Å2
L0.472103027345 °20.16100980705 °2-0.122992824764 °2-1.88248988545 °2-1.74580655183 °2--2.87181132211 °2
S-0.0268948553831 Å °0.0394210541568 Å °-0.0369706677526 Å °0.00857389007388 Å °0.031391452619 Å °-0.0347315283774 Å °-0.0420712659858 Å °-0.221685589843 Å °-0.0105531836597 Å °
Refinement TLS groupSelection details: all

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