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- PDB-2wx0: TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21 -

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Basic information

Entry
Database: PDB / ID: 2wx0
TitleTAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21
Components
  • MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2
  • UBIQUITIN
KeywordsPROTEIN BINDING / ISOPEPTIDE BOND / NZF DOMAIN / ZINC-FINGER / METAL-BINDING
Function / homology
Function and homology information


: / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 ...: / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state
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 conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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 speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKulathu, Y. / Akutsu, M. / Bremm, A. / Hofmann, K. / Komander, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Two-Sided Ubiquitin Binding Explains Specificity of the Tab2 Nzf Domain
Authors: Kulathu, Y. / Akutsu, M. / Bremm, A. / Hofmann, K. / Komander, D.
History
DepositionOct 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
E: UBIQUITIN
F: UBIQUITIN
G: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6908
Polymers41,5606
Non-polymers1312
Water1,856103
1
A: UBIQUITIN
B: UBIQUITIN
C: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8454
Polymers20,7803
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-0.2 kcal/mol
Surface area11460 Å2
MethodPISA
2
E: UBIQUITIN
F: UBIQUITIN
G: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8454
Polymers20,7803
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7.3 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.390, 73.620, 59.250
Angle α, β, γ (deg.)90.00, 105.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UBIQUITIN /


Mass: 8576.831 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P62990, UniProt: P0CH28*PLUS
#2: Protein/peptide MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2 / TAK1-BINDING PROTEIN 2


Mass: 3626.109 Da / Num. of mol.: 2 / Fragment: TAB2 NZF DOMAIN, RESIDUES 663-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9NYJ8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→24.9 Å / Num. obs: 18032 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.799 Å / SU ML: 0.34 / σ(F): 0.02 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 857 5.1 %
Rwork0.1736 --
obs0.1769 16855 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.74 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.425 Å2-0 Å2-2.6818 Å2
2---7.4187 Å20 Å2
3----2.0063 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 2 103 2895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072832
X-RAY DIFFRACTIONf_angle_d1.0993821
X-RAY DIFFRACTIONf_dihedral_angle_d18.21092
X-RAY DIFFRACTIONf_chiral_restr0.071448
X-RAY DIFFRACTIONf_plane_restr0.004494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55040.31881320.23322355X-RAY DIFFRACTION83
2.5504-2.74720.30681360.20912529X-RAY DIFFRACTION90
2.7472-3.02360.3161370.20392645X-RAY DIFFRACTION93
3.0236-3.46090.24051260.18252788X-RAY DIFFRACTION97
3.4609-4.35940.20081510.14332822X-RAY DIFFRACTION99
4.3594-38.80390.18721750.14282859X-RAY DIFFRACTION99
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)
11.1213-0.3432-0.15432.13130.17441.9330.04890.2542-0.0701-0.5081-0.03980.0010.1571-0.0723-0.00380.1280.0511-0.02290.10.00150.021516.096312.81958.683
21.7063-0.38490.55962.9118-3.06853.39230.2749-0.1069-0.1488-0.78910.54370.7190.81-0.6666-0.5410.1725-0.1364-0.11160.18840.13920.246714.2603-6.685230.7969
32.1153-0.8129-1.16710.4530.27491.06880.12640.3536-0.0099-0.0138-0.2279-0.0974-0.2057-0.02660.06270.1712-0.0364-0.03510.10360.02730.156925.05818.174626.4847
41.8344-1.41830.45511.6597-0.24041.05760.43120.58030.3048-0.7218-0.4586-0.16820.17520.0660.08510.28310.16160.04780.23590.01550.1222-12.7104-2.0528.873
50.1662-0.17560.32521.98020.95931.5077-0.031-0.0938-0.0267-0.01320.1888-0.2867-0.07970.1403-0.14250.0648-0.0384-0.01550.1033-0.040.2404-3.162317.042728.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN E
5X-RAY DIFFRACTION5CHAIN F

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