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- PDB-6n5m: Crystal structure of ABIN-1 UBAN in complex with one M1-linked di... -

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Basic information

Entry
Database: PDB / ID: 6n5m
TitleCrystal structure of ABIN-1 UBAN in complex with one M1-linked di-ubiquitin
Components
  • Polyubiquitin-C
  • TNFAIP3-interacting protein 1
KeywordsSIGNALING PROTEIN / Ubiquitin-binding domain / A20-binding protein
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 / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / positive regulation of protein deubiquitination ...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 / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / positive regulation of protein deubiquitination / 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) / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / 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 / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Termination of translesion DNA synthesis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / Senescence-Associated Secretory Phenotype (SASP) / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Oncogene Induced Senescence / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Degradation of AXIN / Regulation of TNFR1 signaling / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / 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 / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Processing of DNA double-strand break ends / Regulation of RUNX2 expression and activity / glycoprotein biosynthetic process / Degradation of GLI1 by the proteasome / Deactivation of the beta-catenin transactivating complex / Ovarian tumor domain proteases
Similarity search - Function
NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsRahighi, S. / Dikic, I. / Wakatsuki, S.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Molecular Recognition of M1-Linked Ubiquitin Chains by Native and Phosphorylated UBAN Domains.
Authors: Herhaus, L. / van den Bedem, H. / Tang, S. / Maslennikov, I. / Wakatsuki, S. / Dikic, I. / Rahighi, S.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Polyubiquitin-C
B: TNFAIP3-interacting protein 1
D: TNFAIP3-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)34,8613
Polymers34,8613
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-38 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.008, 62.109, 123.791
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 Polyubiquitin-C


Mass: 17480.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0CG50
#2: Protein TNFAIP3-interacting protein 1 / A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / Nef-associated factor 1 / Naf1 / Virion- ...A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / Nef-associated factor 1 / Naf1 / Virion-associated nuclear shuttling protein / mVAN


Mass: 8689.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnip1, Abin, Naf1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9WUU8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 20% PEG 3350, 0.2 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→61.9 Å / Num. obs: 6818 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 6.7
Reflection shellResolution: 3.01→3.09 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→61.9 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.853 / SU B: 21.046 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27756 268 4.7 %RANDOM
Rwork0.2394 ---
obs0.24122 5394 83.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.123 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20 Å2
2--1.06 Å20 Å2
3---1.49 Å2
Refinement stepCycle: 1 / Resolution: 3.01→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 22 2277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192270
X-RAY DIFFRACTIONr_bond_other_d0.0030.022232
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9923035
X-RAY DIFFRACTIONr_angle_other_deg0.93135223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86926.239117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88415501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0231516
X-RAY DIFFRACTIONr_chiral_restr0.0630.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02383
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2544.9791101
X-RAY DIFFRACTIONr_mcbond_other1.2494.9771100
X-RAY DIFFRACTIONr_mcangle_it2.0677.4641371
X-RAY DIFFRACTIONr_mcangle_other2.0677.4671372
X-RAY DIFFRACTIONr_scbond_it1.1615.041169
X-RAY DIFFRACTIONr_scbond_other1.1615.0421170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0347.5181665
X-RAY DIFFRACTIONr_long_range_B_refined3.70857.0972428
X-RAY DIFFRACTIONr_long_range_B_other3.70857.1332428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.014→3.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 19 -
Rwork0.291 375 -
obs--82.08 %

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