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- PDB-8w6a: Crystal structure of TAX1BP1 LIR region in complex with GABARAP -

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Basic information

Entry
Database: PDB / ID: 8w6a
TitleCrystal structure of TAX1BP1 LIR region in complex with GABARAP
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Tax1-binding protein 1
KeywordsPROTEIN BINDING / ATG8 / autophagy
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 / positive regulation of protein K48-linked ubiquitination / negative regulation of toll-like receptor 4 signaling pathway / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / phagophore assembly site / TBC/RABGAPs ...protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / positive regulation of protein K48-linked ubiquitination / negative regulation of toll-like receptor 4 signaling pathway / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / phagophore assembly site / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / negative regulation of tumor necrosis factor-mediated signaling pathway / beta-tubulin binding / protein targeting / mitophagy / sperm midpiece / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / GABA-ergic synapse / autophagy / microtubule cytoskeleton organization / kinase binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / protein-macromolecule adaptor activity / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / innate immune response / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Tax1-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsZhang, M.F. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins.
Authors: Zhang, M. / Wang, Y. / Gong, X. / Wang, Y. / Zhang, Y. / Tang, Y. / Zhou, X. / Liu, H. / Huang, Y. / Zhang, J. / Pan, L.
History
DepositionAug 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: Gamma-aminobutyric acid receptor-associated protein
C: Tax1-binding protein 1
D: Gamma-aminobutyric acid receptor-associated protein
E: Tax1-binding protein 1
F: Tax1-binding protein 1
G: Gamma-aminobutyric acid receptor-associated protein
H: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)68,2068
Polymers68,2068
Non-polymers00
Water11,061614
1
A: Gamma-aminobutyric acid receptor-associated protein
C: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,0522
Polymers17,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area8110 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein
E: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,0522
Polymers17,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area8100 Å2
MethodPISA
3
D: Gamma-aminobutyric acid receptor-associated protein
F: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,0522
Polymers17,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area8150 Å2
MethodPISA
4
G: Gamma-aminobutyric acid receptor-associated protein
H: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,0522
Polymers17,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.160, 141.160, 86.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
Gamma-aminobutyric acid receptor-associated protein


Mass: 13942.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP / Production host: Escherichia coli (E. coli) / References: UniProt: O95166
#2: Protein/peptide
Tax1-binding protein 1 / TRAF6-binding protein


Mass: 3109.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VP1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2.8 M Sodium acetate trihydrate and 0.1 M BIS-TRIS propane at pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.53→79.58 Å / Num. obs: 95523 / % possible obs: 99.1 % / Redundancy: 8.1 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.8
Reflection shellResolution: 1.53→1.57 Å / Num. unique obs: 95523 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→26.68 Å / SU ML: 0.1459 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 4898 5.13 %
Rwork0.174 90604 -
obs0.1746 95502 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.25 Å2
Refinement stepCycle: LAST / Resolution: 1.53→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 0 614 5302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01265087
X-RAY DIFFRACTIONf_angle_d1.39216904
X-RAY DIFFRACTIONf_chiral_restr0.1746
X-RAY DIFFRACTIONf_plane_restr0.0132894
X-RAY DIFFRACTIONf_dihedral_angle_d14.35422023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.20161400.22472765X-RAY DIFFRACTION89.17
1.55-1.570.2441680.22482822X-RAY DIFFRACTION93.35
1.57-1.590.20611530.20472889X-RAY DIFFRACTION95.54
1.59-1.610.20551680.2082958X-RAY DIFFRACTION98.3
1.61-1.630.29311560.21083056X-RAY DIFFRACTION99.23
1.63-1.650.1991520.21342979X-RAY DIFFRACTION99.59
1.65-1.670.28852000.22223112X-RAY DIFFRACTION99.91
1.68-1.70.24092040.2052955X-RAY DIFFRACTION99.97
1.7-1.730.22111640.20063081X-RAY DIFFRACTION99.82
1.73-1.750.24181000.20163064X-RAY DIFFRACTION99.87
1.75-1.780.19861720.19323056X-RAY DIFFRACTION99.91
1.79-1.820.19931640.19163024X-RAY DIFFRACTION99.87
1.82-1.850.21851760.18863069X-RAY DIFFRACTION100
1.85-1.890.24261040.19243085X-RAY DIFFRACTION99.97
1.89-1.930.20022000.18152966X-RAY DIFFRACTION99.91
1.93-1.980.19212140.1833040X-RAY DIFFRACTION99.88
1.98-2.020.19761480.17723063X-RAY DIFFRACTION100
2.03-2.080.2143960.17823107X-RAY DIFFRACTION99.94
2.08-2.140.19741840.17743074X-RAY DIFFRACTION100
2.14-2.210.16681400.17643048X-RAY DIFFRACTION99.91
2.21-2.290.16612520.17032940X-RAY DIFFRACTION99.97
2.29-2.380.21471920.18463035X-RAY DIFFRACTION100
2.38-2.490.20331520.17763044X-RAY DIFFRACTION100
2.49-2.620.17531280.18243128X-RAY DIFFRACTION99.91
2.62-2.780.15541760.17493044X-RAY DIFFRACTION100
2.79-30.21631720.17992970X-RAY DIFFRACTION99.97
3-3.30.17231240.16373094X-RAY DIFFRACTION99.97
3.3-3.770.18491720.1553028X-RAY DIFFRACTION99.94
3.78-4.750.14262160.13433021X-RAY DIFFRACTION99.88
4.76-26.680.17161110.16933087X-RAY DIFFRACTION99.35

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