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- PDB-5yt6: Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5yt6
TitleCrystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin
Components
  • Tax1-binding protein 1
  • Ubiquitin
KeywordsPROTEIN BINDING / TAX1BP1 / ubiquitin / complex / autophagy receptor
Function / homology
Function and homology information


protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule ...protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of tumor necrosis factor-mediated signaling pathway / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / signaling adaptor activity / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of canonical NF-kappaB signal transduction / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / autophagosome / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / regulation of mitochondrial membrane potential / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A
Similarity search - Function
Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / : / Ubiquitin domain signature. ...Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / : / 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-B / Tax1-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsPan, L. / Hu, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470749 China
National Key R&D Program of China2016YFA0501903 China
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Mechanistic Insights into Recognitions of Ubiquitin and Myosin VI by Autophagy Receptor TAX1BP1.
Authors: Hu, S. / Wang, Y. / Gong, Y. / Liu, J. / Li, Y. / Pan, L.
History
DepositionNov 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
E: Ubiquitin
F: Tax1-binding protein 1
A: Ubiquitin
B: Tax1-binding protein 1
C: Ubiquitin
D: Tax1-binding protein 1
G: Ubiquitin
H: Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,52316
Polymers51,9158
Non-polymers6088
Water6,431357
1
E: Ubiquitin
F: Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0443
Polymers12,9792
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ubiquitin
B: Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1404
Polymers12,9792
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin
D: Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1404
Polymers12,9792
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ubiquitin
H: Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1985
Polymers12,9792
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.709, 72.938, 119.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 8 molecules EACGFBDH

#1: Protein
Ubiquitin


Mass: 8720.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0CG47
#2: Protein/peptide
Tax1-binding protein 1 / TRAF6-binding protein


Mass: 4257.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP1, T6BP, PRO0105
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q86VP1

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Non-polymers , 5 types, 365 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, BIS TRIS propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 68493 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.056 / Rrim(I) all: 0.137 / Χ2: 0.882 / Net I/σ(I): 5.9 / Num. measured all: 419962
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.533.90.46531400.7630.2630.5380.6992
1.53-1.554.40.39733040.8370.210.4520.68297.6
1.55-1.585.20.36333730.8830.1750.4050.70498.5
1.58-1.626.50.34334090.9050.1460.3740.73899.8
1.62-1.656.70.31733890.9310.1320.3440.77199.9
1.65-1.696.70.2934150.9380.1210.3150.81799.9
1.69-1.736.60.26734090.9410.1120.290.87599.9
1.73-1.786.50.24534030.9420.1040.2660.92299.9
1.78-1.8360.21834100.9510.0960.2390.99499.8
1.83-1.896.70.20634130.9520.0860.2241.00299.9
1.89-1.966.70.20334220.9560.0840.221.09199.9
1.96-2.046.60.17934510.9620.0760.1951.05899.8
2.04-2.136.40.15834250.9720.0680.1720.98199.9
2.13-2.246.10.14734320.9730.0650.1610.97599.9
2.24-2.386.60.14234360.980.060.1540.95499.7
2.38-2.566.50.13434790.980.0570.1460.92199.8
2.56-2.8260.12434700.9790.0550.1360.91199.7
2.82-3.236.50.11734940.9820.0510.1280.84899.7
3.23-4.0760.10435260.9860.0470.1140.7899.4
4.07-505.80.09736930.9890.0440.1070.69599.1

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMJ

4bmj


Resolution: 1.501→30.894 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 3428 5.07 %RANDOM
Rwork0.1934 ---
obs0.195 67619 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.11 Å2 / Biso mean: 17.5884 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.501→30.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 24 357 3878
Biso mean--23.87 25.51 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063601
X-RAY DIFFRACTIONf_angle_d0.94870
X-RAY DIFFRACTIONf_chiral_restr0.06552
X-RAY DIFFRACTIONf_plane_restr0.006634
X-RAY DIFFRACTIONf_dihedral_angle_d17.882224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5015-1.52290.25651080.23642149225779
1.5229-1.54560.23851040.22812440254491
1.5456-1.56980.27071550.2112566272195
1.5698-1.59550.25551430.2032650279398
1.5955-1.6230.23161570.192126852842100
1.623-1.65250.20711260.185326812807100
1.6525-1.68430.27481690.18726662835100
1.6843-1.71870.20841340.197326752809100
1.7187-1.75610.21471560.193326982854100
1.7561-1.79690.24071550.184426892844100
1.7969-1.84190.23921320.19326802812100
1.8419-1.89160.21831410.190327012842100
1.8916-1.94730.21531420.192127272869100
1.9473-2.01010.25111480.193226892837100
2.0101-2.0820.21911400.194227222862100
2.082-2.16530.25181390.19126872826100
2.1653-2.26380.23231420.19142739288199
2.2638-2.38310.22051470.19362703285099
2.3831-2.53240.22491420.204327452887100
2.5324-2.72780.21611370.20692732286999
2.7278-3.00210.22591630.21192726288999
3.0021-3.4360.22561360.20292774291099
3.436-4.32720.21021350.17122801293699
4.3272-30.90040.20921770.18062866304398

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