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- PDB-7eb9: The structure of the A20-binding inhibitor of NF-kB 1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 7eb9
TitleThe structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin
Components
  • TNFAIP3-interacting protein 1
  • tetra ubiquitin
KeywordsSIGNALING PROTEIN / A20-binding inhibitor of NF-kB / ubiquitin
Function / homology
Function and homology information


positive regulation of protein deubiquitination / glycoprotein biosynthetic process / mitogen-activated protein kinase binding / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / negative regulation of canonical NF-kappaB signal transduction / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...positive regulation of protein deubiquitination / glycoprotein biosynthetic process / mitogen-activated protein kinase binding / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / negative regulation of canonical NF-kappaB signal transduction / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Defective CFTR causes cystic fibrosis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Stabilization of p53 / EGFR downregulation
Similarity search - Function
Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / TNFAIP3-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLo, Y.C. / Lin, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 107-2320-B-006 -062 -MY3 Taiwan
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-kappa B 1 (ABIN1) and M1-Linked Ubiquitins.
Authors: Hong, J.Y. / Lin, S.C. / Kuo, B.J. / Lo, Y.C.
History
DepositionMar 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tetra ubiquitin
B: TNFAIP3-interacting protein 1
C: TNFAIP3-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)57,0473
Polymers57,0473
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-31 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.381, 53.777, 240.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein tetra ubiquitin


Mass: 34253.301 Da / Num. of mol.: 1
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 1 / A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / HIV-1 Nef-interacting protein / Nef- ...A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / HIV-1 Nef-interacting protein / Nef-associated factor 1 / Naf1 / Nip40-1 / Virion-associated nuclear shuttling protein / VAN / hVAN


Mass: 11396.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIP1, KIAA0113, NAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15025

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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: 2.57 Å3/Da / Density % sol: 52.1 % / Description: Needle shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Sodium malonate pH 6.0, 10% PEG 3350

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 3.2→26 Å / Num. obs: 10149 / % possible obs: 96.29 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.4
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.47 / Num. unique obs: 790

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EAO

7eao


Resolution: 3.2→26 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 982 9.68 %
Rwork0.2165 --
obs0.2211 10149 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 0 0 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023362
X-RAY DIFFRACTIONf_angle_d0.4824509
X-RAY DIFFRACTIONf_dihedral_angle_d8.0132135
X-RAY DIFFRACTIONf_chiral_restr0.039525
X-RAY DIFFRACTIONf_plane_restr0.003589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.34640.36591290.30121081X-RAY DIFFRACTION83
3.3464-3.55570.31551450.2551255X-RAY DIFFRACTION95
3.5557-3.82950.32131250.25261314X-RAY DIFFRACTION98
3.8295-4.21360.25911240.20531347X-RAY DIFFRACTION99
4.2136-4.82050.23831560.19131330X-RAY DIFFRACTION100
4.8205-6.06240.22531510.2251372X-RAY DIFFRACTION100
6.0624-100.24131520.18761468X-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)
16.2899-0.3875-3.12176.16710.95024.1064-0.177-1.9011-0.63330.9315-0.06770.7642-0.07-0.20620.160.54940.15810.14851.06090.07760.5252-7.3343-5.225757.7466
29.4597-2.12191.46693.52591.54884.34440.3388-0.0278-0.6477-0.0694-0.1519-0.48920.1240.1922-0.19920.17260.07590.05260.37920.14290.7004-20.884737.650536.4103
37.24162.0616-0.15962.91440.95574.911-0.17410.978-0.9635-0.7392-0.0073-0.12421.14160.34070.12320.79720.13080.0470.6651-0.12120.5914-41.744937.01815.9065
44.6706-2.26523.32141.9019-5.13656.2017-0.3097-0.4716-0.0202-0.1944-0.1715-0.0743-0.5487-1.7445-0.02620.42430.0713-0.00850.4953-0.03040.3375-2.7846-6.067430.4931
57.9233-6.69877.97156.3859-7.46148.4696-0.18410.78070.72330.0206-0.9059-0.6892-0.50561.06770.60770.43150.0153-0.0430.47760.0660.48383.5001-2.739832.8071
65.6499-1.0217-0.39099.5518-0.95721.4088-0.23180.12030.63590.46410.22620.3697-0.645-0.27540.02860.56510.2367-0.08230.5318-0.04650.4244-8.407614.389735.021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 276)
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 371 )
4X-RAY DIFFRACTION4chain 'B' and (resid 452 through 505 )
5X-RAY DIFFRACTION5chain 'C' and (resid 446 through 505 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 176 )

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