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- PDB-5jhf: Crystal structure of Atg13(17BR)-Atg13(17LR)-Atg17-Atg29-Atg31 complex -

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Basic information

Entry
Database: PDB / ID: 5jhf
TitleCrystal structure of Atg13(17BR)-Atg13(17LR)-Atg17-Atg29-Atg31 complex
Components
  • Atg13 17BR
  • Atg13 17LR
  • KLTH0C07942p
  • KLTH0D11660p
  • KLTH0D15642p
KeywordsPROTEIN TRANSPORT / coiled-coil
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / protein kinase activator activity / mitophagy / autophagosome assembly / autophagy / protein transport ...Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / protein kinase activator activity / mitophagy / autophagosome assembly / autophagy / protein transport / molecular adaptor activity / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #2570 / Autophagy-related protein 31 / Autophagy-related protein 17 / Autophagy-related protein 31 / Autophagy-related protein 29 / Autophagy-related protein 29 superfamily / Atg29, N-terminal / Autophagy-related protein 31 / Atg29 N-terminal domain / Autophagy protein ATG17-like domain ...Arc Repressor Mutant, subunit A - #2570 / Autophagy-related protein 31 / Autophagy-related protein 17 / Autophagy-related protein 31 / Autophagy-related protein 29 / Autophagy-related protein 29 superfamily / Atg29, N-terminal / Autophagy-related protein 31 / Atg29 N-terminal domain / Autophagy protein ATG17-like domain / Autophagy protein ATG17-like domain / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Mutm (Fpg) Protein; Chain: A, domain 2 / HORMA domain superfamily / Arc Repressor Mutant, subunit A / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Autophagy-related protein 13 / KLTH0C07942p / Autophagy-related protein 29 / Autophagy-related protein 17
Similarity search - Component
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsFujioka, Y. / Noda, N.N.
CitationJournal: Dev.Cell / Year: 2016
Title: The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes.
Authors: Yamamoto, H. / Fujioka, Y. / Suzuki, S.W. / Noshiro, D. / Suzuki, H. / Kondo-Kakuta, C. / Kimura, Y. / Hirano, H. / Ando, T. / Noda, N.N. / Ohsumi, Y.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLTH0D11660p
B: KLTH0C07942p
C: KLTH0D15642p
D: KLTH0D11660p
E: KLTH0C07942p
F: KLTH0D15642p
G: Atg13 17BR
H: Atg13 17BR
I: Atg13 17LR
J: Atg13 17LR


Theoretical massNumber of molelcules
Total (without water)158,00910
Polymers158,00910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22880 Å2
ΔGint-144 kcal/mol
Surface area67560 Å2
MethodPISA
2
A: KLTH0D11660p
B: KLTH0C07942p
C: KLTH0D15642p
G: Atg13 17BR
I: Atg13 17LR


Theoretical massNumber of molelcules
Total (without water)79,0045
Polymers79,0045
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-55 kcal/mol
Surface area36520 Å2
MethodPISA
3
D: KLTH0D11660p
E: KLTH0C07942p
F: KLTH0D15642p
H: Atg13 17BR
J: Atg13 17LR


Theoretical massNumber of molelcules
Total (without water)79,0045
Polymers79,0045
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-54 kcal/mol
Surface area36980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.956, 64.043, 184.387
Angle α, β, γ (deg.)90.00, 109.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA1 - 821 - 82
21METMETGLUGLUDD1 - 821 - 82
12VALVALHISHISBB9 - 1469 - 146
22VALVALHISHISEE9 - 1469 - 146
13METMETVALVALCC1 - 4131 - 413
23METMETVALVALFF1 - 4131 - 413

NCS ensembles :
ID
1
2
3

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Components

#1: Protein KLTH0D11660p / Atg29


Mass: 10493.102 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0D11660g / Production host: Escherichia coli (E. coli) / References: UniProt: C5DF24
#2: Protein KLTH0C07942p / Atg31


Mass: 17387.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0C07942g / Production host: Escherichia coli (E. coli) / References: UniProt: C5DEB9
#3: Protein KLTH0D15642p / Atg17


Mass: 48312.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0D15642g / Production host: Escherichia coli (E. coli) / References: UniProt: C5DFJ6
#4: Protein/peptide Atg13 17BR


Mass: 1575.774 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: C5DB94*PLUS
#5: Protein/peptide Atg13 17LR


Mass: 1235.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: C5DB94*PLUS

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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: 5.2 Å3/Da / Density % sol: 76.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5% polyethylene glycol monomethyl ether 5000, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 53805 / % possible obs: 99.9 % / Redundancy: 5.3 % / Net I/σ(I): 16.3
Reflection shellResolution: 3.2→3.26 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P1W

4p1w


Resolution: 3.21→49.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 40.235 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.696 / ESU R Free: 0.385 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 2700 5.1 %RANDOM
Rwork0.22393 ---
obs0.22596 50369 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 142.453 Å2
Baniso -1Baniso -2Baniso -3
1-5.66 Å20 Å27.59 Å2
2---0.08 Å2-0 Å2
3----6.6 Å2
Refinement stepCycle: 1 / Resolution: 3.21→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9843 0 0 0 9843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199991
X-RAY DIFFRACTIONr_bond_other_d0.0040.029549
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.94913521
X-RAY DIFFRACTIONr_angle_other_deg1.105321840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23851246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18525.04502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.037151707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5741563
X-RAY DIFFRACTIONr_chiral_restr0.0890.21555
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211506
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022321
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_it6.7828.2285032
X-RAY DIFFRACTIONr_mcbond_other6.7828.2265031
X-RAY DIFFRACTIONr_mcangle_it10.23712.3286262
X-RAY DIFFRACTIONr_mcangle_other10.23712.336263
X-RAY DIFFRACTIONr_scbond_it7.8348.5224959
X-RAY DIFFRACTIONr_scbond_other7.8338.5244960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.18412.5767260
X-RAY DIFFRACTIONr_long_range_B_refined15.26763.70111540
X-RAY DIFFRACTIONr_long_range_B_other15.26763.71111541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A28900.15
12D28900.15
21B66880.08
22E66880.08
31C215250.13
32F215250.13
LS refinement shellResolution: 3.209→3.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 169 -
Rwork0.326 3182 -
obs--85.59 %
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)
15.69780.8645-1.84098.21740.97146.44640.0379-0.56581.38841.29220.27540.0437-1.41810.1613-0.31331.30960.0111-0.17170.9018-0.07151.227912.88524.846520.9603
24.42653.1501-0.96878.7184-2.15972.6927-0.159-0.4710.24220.244-0.1813-0.6122-0.55220.43780.34030.56280.1098-0.090.38750.00220.2917.93099.44415.531
30.16710.1144-0.05230.3658-0.25530.7923-0.1948-0.10950.014-0.1848-0.1524-0.07610.33030.2230.34720.37110.09020.10240.28460.08870.1668-8.5192-2.687631.9646
44.4733-1.732-2.611410.5058-0.84634.2256-0.17810.3293-0.2275-0.00740.3467-1.55471.34490.1575-0.16861.21060.1285-0.22681.441-0.07711.5748-112.7869-10.3549182.1013
53.38510.904-1.39858.2475-3.03385.19770.0975-0.5032-0.62240.40450.0039-0.51040.20680.4651-0.10140.15640.0351-0.12510.5777-0.16430.7224-121.00555.6722178.4589
61.3329-0.2308-0.65230.16330.1270.63670.1443-0.35760.2765-0.06970.06360.06820.04860.2987-0.20790.311-0.05870.29030.3677-0.16130.68-107.270517.0896157.4192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 82
2X-RAY DIFFRACTION2B9 - 146
3X-RAY DIFFRACTION3C1 - 413
4X-RAY DIFFRACTION4D1 - 82
5X-RAY DIFFRACTION5E9 - 146
6X-RAY DIFFRACTION6F1 - 413

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