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- PDB-6n6r: Crystal structure of ABIN-1 UBAN in complex with two M1-linked di... -

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Basic information

Entry
Database: PDB / ID: 6n6r
TitleCrystal structure of ABIN-1 UBAN in complex with two M1-linked di-ubiquitins
Components
  • TNFAIP3-interacting protein 1
  • Ubiquitin
KeywordsSIGNALING PROTEIN / Ubiquitin-binding domain / A20-binding protein / Ubiquitin
Function / homology
Function and homology information


positive regulation of protein deubiquitination / glycoprotein biosynthetic process / Ovarian tumor domain proteases / mitogen-activated protein kinase binding / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / polyubiquitin modification-dependent protein binding / negative regulation of canonical NF-kappaB signal transduction / Maturation of protein E / Maturation of protein E ...positive regulation of protein deubiquitination / glycoprotein biosynthetic process / Ovarian tumor domain proteases / mitogen-activated protein kinase binding / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / polyubiquitin modification-dependent protein binding / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / 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 / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / Termination of translesion DNA synthesis / Peroxisomal protein import / 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 / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Stabilization of p53
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 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 27, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: TNFAIP3-interacting protein 1
D: TNFAIP3-interacting protein 1
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)52,0534
Polymers52,0534
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-40 kcal/mol
Surface area23290 Å2
Unit cell
Length a, b, c (Å)52.900, 88.180, 105.900
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: 17480.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0CG48
#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: 8545.683 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.: 135 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% v/v PEG-MME550, 0.1 M bis-tris pH 6.5, and 0.05 M calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→67.76 Å / Num. obs: 36800 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2566 / CC1/2: 0.853 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.982 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27786 1890 5.1 %RANDOM
Rwork0.24348 ---
obs0.24529 34847 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.95→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 0 135 3653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193546
X-RAY DIFFRACTIONr_bond_other_d0.0060.023497
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9944749
X-RAY DIFFRACTIONr_angle_other_deg0.90338181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87326.136176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50715772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6281524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
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_it1.1252.8481728
X-RAY DIFFRACTIONr_mcbond_other1.1262.8481727
X-RAY DIFFRACTIONr_mcangle_it2.0394.2572153
X-RAY DIFFRACTIONr_mcangle_other2.0394.2572154
X-RAY DIFFRACTIONr_scbond_it0.9633.0221818
X-RAY DIFFRACTIONr_scbond_other0.9633.0221819
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8284.4542597
X-RAY DIFFRACTIONr_long_range_B_refined4.30933.0333711
X-RAY DIFFRACTIONr_long_range_B_other4.28232.9473697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 142 -
Rwork0.287 2545 -
obs--100 %
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)
10.83680.09710.79570.22230.49462.4890.03190.0888-0.1298-0.0310.0149-0.0750.0285-0.0562-0.04680.0207-0.0122-0.00190.036-0.02920.128317.8324-36.558115.4883
20.1428-0.08640.19350.3406-1.6128.2747-0.016-0.020.01640.01160.0065-0.0233-0.1654-0.03330.00950.0860.01810.01320.0080.01280.072515.5078-20.904832.7816
30.1008-0.0674-0.29470.09630.38578.0329-0.00840.00470.0203-0.0196-0.01370.04210.02910.06810.02210.08120.0454-0.00610.02720.0020.075910.3813-20.382733.7646
40.27380.2742-0.6540.279-0.63822.593600.03390.1419-0.02240.03960.1462-0.0685-0.0085-0.03960.04820.0049-0.02250.01290.040.18375.3131-2.240618.5668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 148
2X-RAY DIFFRACTION2B464 - 531
3X-RAY DIFFRACTION3D465 - 531
4X-RAY DIFFRACTION4C1 - 150

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