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- PDB-5h07: TNIP2-Ub complex, C2 form -

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Basic information

Entry
Database: PDB / ID: 5h07
TitleTNIP2-Ub complex, C2 form
Components
  • Polyubiquitin-C
  • TNFAIP3-interacting protein 2
KeywordsSIGNALING PROTEIN / coiled-coil / complex / signal transduction
Function / homology
Function and homology information


toll-like receptor 2 signaling pathway / CD40 signaling pathway / positive regulation of B cell activation / toll-like receptor 3 signaling pathway / toll-like receptor 9 signaling pathway / positive regulation of macrophage activation / interleukin-1-mediated signaling pathway / K63-linked polyubiquitin modification-dependent protein binding / protein deubiquitination / polyubiquitin modification-dependent protein binding ...toll-like receptor 2 signaling pathway / CD40 signaling pathway / positive regulation of B cell activation / toll-like receptor 3 signaling pathway / toll-like receptor 9 signaling pathway / positive regulation of macrophage activation / interleukin-1-mediated signaling pathway / K63-linked polyubiquitin modification-dependent protein binding / protein deubiquitination / polyubiquitin modification-dependent protein binding / stress-activated MAPK cascade / negative regulation of endothelial cell apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells
Similarity search - Function
TSG101 and ALIX binding domain of CEP55 / TSG101 and ALIX binding domain of CEP55 / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain ...TSG101 and ALIX binding domain of CEP55 / TSG101 and ALIX binding domain of CEP55 / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / TNFAIP3-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.586 Å
AuthorsLo, Y.C. / Lin, S.C.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and TechnologyNSC 101-2311-B-006-008-MY3 Taiwan
Ministry of Science and TechnologyMOST 104-2320-B-006-033-MY3 Taiwan
Taiwan Protein ProjectMOST 105-0210-01-12-01 Taiwan
CitationJournal: Structure / Year: 2017
Title: Structural Insights into Linear Tri-ubiquitin Recognition by A20-Binding Inhibitor of NF-kappa B, ABIN-2
Authors: Lin, S.M. / Lin, S.C. / Hong, J.Y. / Su, T.W. / Kuo, B.J. / Chang, W.H. / Tu, Y.F. / Lo, Y.C.
History
DepositionOct 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-C
D: TNFAIP3-interacting protein 2
C: TNFAIP3-interacting protein 2


Theoretical massNumber of molelcules
Total (without water)47,1293
Polymers47,1293
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-36 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.765, 80.972, 65.352
Angle α, β, γ (deg.)90.00, 114.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polyubiquitin-C


Mass: 25694.496 Da / Num. of mol.: 1 / Fragment: UNP residues 1-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein TNFAIP3-interacting protein 2 / A20-binding inhibitor of NF-kappa-B activation 2 / ABIN-2 / Fetal liver LKB1-interacting protein


Mass: 10717.009 Da / Num. of mol.: 2 / Fragment: UNP residues 257-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIP2, ABIN2, FLIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NFZ5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, PEG3350, Tris-HCl

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.586→30 Å / Num. obs: 12803 / % possible obs: 99.2 % / Redundancy: 3.5 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.586→19.858 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.25
RfactorNum. reflection% reflection
Rfree0.2734 1280 10.01 %
Rwork0.2113 --
obs0.2177 12791 86.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.586→19.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 0 98 3027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022954
X-RAY DIFFRACTIONf_angle_d0.5173965
X-RAY DIFFRACTIONf_dihedral_angle_d13.5491175
X-RAY DIFFRACTIONf_chiral_restr0.02462
X-RAY DIFFRACTIONf_plane_restr0.002521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5859-2.68920.2834610.2299547X-RAY DIFFRACTION37
2.6892-2.81120.3919970.242869X-RAY DIFFRACTION60
2.8112-2.9590.31981450.24081308X-RAY DIFFRACTION89
2.959-3.14370.30371630.25241470X-RAY DIFFRACTION99
3.1437-3.38530.31111620.23561463X-RAY DIFFRACTION100
3.3853-3.7240.27931640.21071469X-RAY DIFFRACTION100
3.724-4.25820.24531640.18421476X-RAY DIFFRACTION99
4.2582-5.34750.24621630.17651466X-RAY DIFFRACTION99
5.3475-19.85830.23751610.21761443X-RAY DIFFRACTION96
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)
10.36550.09870.16543.15153.7436.3496-0.11610.1888-0.11540.099-0.04670.1525-0.0632-0.31520.38530.1915-0.0024-0.12610.345-0.11960.284613.812534.271133.5894
21.99792.07190.47688.82062.6095.8369-0.1671-0.9102-0.0450.58840.09960.3215-0.3698-0.27640.05520.79570.09280.00710.68460.08380.702925.046849.849186.8862
30.5237-0.167-0.30421.59811.94.4035-0.14060.2307-0.2083-0.13310.20510.16660.05540.08390.14570.2396-0.071-0.11890.2995-0.12410.283819.108235.608832.1668
46.30230.3614-0.39783.14730.36653.4498-0.2254-0.946-0.41370.24740.01320.06540.01610.19080.20.38230.1267-0.10370.3114-0.0210.351831.842130.305846.2496
52.01211.87050.54293.867-0.2142.1395-0.0137-0.0254-0.271-0.01920.4562-1.07450.50010.1449-0.35280.4007-0.0748-0.08380.4186-0.25620.621921.289110.769928.0636
63.8065-0.11183.67633.0953-1.18983.93020.2176-1.41760.14790.91610.0926-0.32880.0648-0.0252-0.26170.6855-0.0401-0.15671.5705-0.14320.658510.26432.730251.7634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and ((resseq 274:339))
2X-RAY DIFFRACTION2chain 'D' and ((resseq 262:274))
3X-RAY DIFFRACTION3chain 'D' and ((resseq 275:339))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 1:76))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 101:176))
6X-RAY DIFFRACTION6chain 'A' and ((resseq 201:271))

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