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- PDB-5xv6: Crystal structure of ATG101-ATG13HORMA -

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Basic information

Entry
Database: PDB / ID: 5xv6
TitleCrystal structure of ATG101-ATG13HORMA
Components
  • Autophagy-related protein 101
  • Autophagy-related protein 13
KeywordsPROTEIN BINDING / AUTOPHAGY / ATG101 / ATG13 / HORMA
Function / homology
Function and homology information


regulation of protein lipidation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / positive regulation of protein targeting to mitochondrion / Macroautophagy ...regulation of protein lipidation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / positive regulation of protein targeting to mitochondrion / Macroautophagy / mitophagy / autophagosome assembly / autophagosome / positive regulation of autophagy / protein serine/threonine kinase activator activity / negative regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 101 / Autophagy-related protein 101 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 13 / Autophagy-related protein 101
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 Å
AuthorsKim, B.-W. / Song, H.K.
CitationJournal: Autophagy / Year: 2018
Title: The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation.
Authors: Kim, B.-W. / Jin, Y. / Kim, J. / Kim, J.H. / Jung, J. / Kang, S. / Kim, I.Y. / Kim, J. / Cheong, H. / Song, H.K.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 13
B: Autophagy-related protein 101


Theoretical massNumber of molelcules
Total (without water)46,1822
Polymers46,1822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, 1:1 heterodimer, SAXS, 1:1 heterodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-13 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.019, 123.485, 99.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Autophagy-related protein 13 /


Mass: 21319.652 Da / Num. of mol.: 1 / Fragment: UNP residues 1-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Escherichia coli (E. coli) / References: UniProt: O75143
#2: Protein Autophagy-related protein 101 /


Mass: 24862.424 Da / Num. of mol.: 1 / Mutation: K40A/K41A/E42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG101, C12orf44, PP894 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSB4

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 19228 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 64.06 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Χ2: 1.575 / Net I/av σ(I): 33.39 / Net I/σ(I): 8.1 / Num. measured all: 136207
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.44-2.487.10.9129460.8110.3630.9840.53199.3
2.48-2.537.30.7689470.8580.3030.8280.53999.8
2.53-2.5870.5989410.9070.2420.6470.602100
2.58-2.637.50.5489600.9180.2140.590.60899.9
2.63-2.697.60.4619420.9360.1790.4960.619100
2.69-2.757.60.3979590.9530.1540.4260.686100
2.75-2.827.40.3339480.9560.1320.3590.735100
2.82-2.897.30.299490.9650.1150.3130.81100
2.89-2.986.90.2299690.9770.0940.2480.99399.8
2.98-3.077.40.1929490.9810.0760.2071.08100
3.07-3.1870.1519580.9890.0620.1631.307100
3.18-3.317.40.1349570.9870.0530.1451.471100
3.31-3.467.40.1129520.9920.0450.1211.7199.9
3.46-3.647.30.1039760.9920.0410.1112.13699.8
3.64-3.876.70.0899650.9960.0370.0972.60799.7
3.87-4.176.90.0769590.9960.0320.0832.83699.1
4.17-4.596.90.0729570.9950.030.0783.24398.5
4.59-5.256.50.0689720.9950.0290.0743.18398.7
5.25-6.626.40.079840.9950.0290.0763.08298.9
6.62-506.20.0610380.9950.0270.0663.46898.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUY

5xuy


Resolution: 2.455→49.899 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.12
RfactorNum. reflection% reflection
Rfree0.2711 1918 10 %
Rwork0.2246 --
obs0.2291 19189 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.23 Å2 / Biso mean: 77.5409 Å2 / Biso min: 38.17 Å2
Refinement stepCycle: final / Resolution: 2.455→49.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 0 0 3017
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093068
X-RAY DIFFRACTIONf_angle_d1.14167
X-RAY DIFFRACTIONf_chiral_restr0.062498
X-RAY DIFFRACTIONf_plane_restr0.006526
X-RAY DIFFRACTIONf_dihedral_angle_d17.3881831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.455-2.51640.35251300.30511174130496
2.5164-2.58440.31711360.289212201356100
2.5844-2.66050.36381370.279812291366100
2.6605-2.74630.34261350.282812171352100
2.7463-2.84450.33811350.288912301365100
2.8445-2.95840.38221370.275212321369100
2.9584-3.0930.37221380.280112341372100
3.093-3.2560.28951380.25712431381100
3.256-3.460.25371350.231812221357100
3.46-3.7270.29371400.247112441384100
3.727-4.1020.2591350.20871231136699
4.102-4.69510.21261370.19161238137598
4.6951-5.91390.28771410.20941255139699
5.9139-49.90930.22791440.19671302144698

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