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- PDB-3a9j: Crystal structure of the mouse TAB2-NZF in complex with Lys63-lin... -

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Basic information

Entry
Database: PDB / ID: 3a9j
TitleCrystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin
Components
  • (Ubiquitin) x 2
  • Mitogen-activated protein kinase kinase kinase 7-interacting protein 2
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / protein complex / Cytoplasm / Isopeptide bond / Metal-binding / Zinc / Zinc-finger / SIGNALING PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


: / : / 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 ...: / : / 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 / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity
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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å
AuthorsSato, Y. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Fukai, S.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3
Authors: Sato, Y. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Fukai, S.
History
DepositionOct 29, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Mitogen-activated protein kinase kinase kinase 7-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2254
Polymers21,1593
Non-polymers651
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.085, 71.478, 72.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCHAINS A AND B ARE COVALENTLY BONDED TO FORM A SINGLE MOLECULE. THIS MOLECULE FORM A HETERO DIMERIC COMPLEX WITH CHAIN C.

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Components

#1: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubiquitin / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62991, UniProt: P0CG50*PLUS
#2: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: 77D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubiquitin / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62991, UniProt: P0CG50*PLUS
#3: Protein/peptide Mitogen-activated protein kinase kinase kinase 7-interacting protein 2 / TAK1-binding protein 2 / TAB2


Mass: 3862.468 Da / Num. of mol.: 1 / Fragment: RanBP2-type, residues 665-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TAB2 (AMINO ACIDS 665 - 693) / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q99K90
#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.: 205 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 90mM Bis-Tris-HCl (pH 6.5), 180mM ammonium acetate, 21% PE3350, 4% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 29, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. all: 52096 / Num. obs: 52096 / % possible obs: 96 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.046 / Net I/σ(I): 55.5
Reflection shellResolution: 1.18→1.19 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.05 / % possible all: 88.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.18→36.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.544 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19097 2557 5.1 %RANDOM
Rwork0.16436 ---
obs0.16573 47387 96.07 %-
all-52096 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.196 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2--0.83 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.18→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 1 205 1706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221530
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9782068
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47824.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3111512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021142
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2622
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1061.5963
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1121528
X-RAY DIFFRACTIONr_scbond_it3.843613
X-RAY DIFFRACTIONr_scangle_it5.6374.5536
X-RAY DIFFRACTIONr_rigid_bond_restr2.05931576
X-RAY DIFFRACTIONr_sphericity_free10.8113205
X-RAY DIFFRACTIONr_sphericity_bonded9.73331501
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 160 -
Rwork0.224 3192 -
obs--88.87 %

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