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- PDB-2wwz: TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121 -

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Basic information

Entry
Database: PDB / ID: 2wwz
TitleTAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121
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 / Processing of DNA double-strand break ends / 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 / DNA Damage Recognition in GG-NER / Activation of NF-kappaB in B cells / 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 / 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 / TNFR2 non-canonical NF-kB pathway
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 domain / Ubiquitin-like (UB roll) / 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 speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 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
Revision 1.3Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9604
Polymers20,8953
Non-polymers651
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-5 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.980, 69.610, 71.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN


Mass: 8576.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) 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: 3741.196 Da / Num. of mol.: 1 / Fragment: TAB2 NZF DOMAIN, RESIDUES 662-693
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.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.6 Å3/Da / Density % sol: 22.31 % / 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: 1.4→23.4 Å / Num. obs: 30078 / % possible obs: 96.4 % / Observed criterion σ(I): 1.8 / Redundancy: 3.4 % / Biso Wilson estimate: 13.23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.4→22.193 Å / SU ML: 0.16 / σ(F): 0.03 / Phase error: 20.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2018 1453 5.1 %
Rwork0.1779 --
obs0.1792 28619 91.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.078 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1841 Å20 Å20 Å2
2--2.1149 Å20 Å2
3----0.9308 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 1 214 1643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061546
X-RAY DIFFRACTIONf_angle_d1.0822107
X-RAY DIFFRACTIONf_dihedral_angle_d15.052633
X-RAY DIFFRACTIONf_chiral_restr0.071245
X-RAY DIFFRACTIONf_plane_restr0.005277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.297960.26591870X-RAY DIFFRACTION64
1.45-1.50810.25461100.23142382X-RAY DIFFRACTION82
1.5081-1.57670.21351420.19932624X-RAY DIFFRACTION90
1.5767-1.65980.23761440.18742766X-RAY DIFFRACTION93
1.6598-1.76380.19591610.17422733X-RAY DIFFRACTION95
1.7638-1.89990.21571280.17312871X-RAY DIFFRACTION96
1.8999-2.09090.20861680.1632878X-RAY DIFFRACTION98
2.0909-2.39320.1981490.1662957X-RAY DIFFRACTION99
2.3932-3.0140.20621610.17592989X-RAY DIFFRACTION100
3.014-22.1960.18131940.17083096X-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)
11.46850.28580.61150.6717-0.08710.83460.08480.0667-0.2285-0.0175-0.0049-0.0847-0.02190.0858-0.06940.06520.0070.00030.11020.00770.116213.474315.675512.7194
20.7575-0.068-0.59881.0789-0.10640.95790.02470.094-0.04240.0016-0.0703-0.0052-0.0098-0.07250.03970.10360.01110.01120.11-0.00810.069212.006138.6648-4.2793
30.0967-0.0037-0.18351.08030.10.5459-0.00650.01760.0260.02840.00640.18570.0233-0.1041-0.01040.09440.00350.0180.11510.01490.09771.586432.18069.8553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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