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- PDB-4p1n: Crystal structure of Atg1-Atg13 complex -

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Basic information

Entry
Database: PDB / ID: 4p1n
TitleCrystal structure of Atg1-Atg13 complex
Components
  • Atg1 tMIT
  • Atg13 MIM
KeywordsPROTEIN TRANSPORT / Complex
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / response to starvation / autophagosome assembly / mitophagy ...Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / response to starvation / autophagosome assembly / mitophagy / autophagosome / protein transport / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of autophagy / protein serine kinase activity / ATP binding / cytosol
Similarity search - Function
Helix Hairpins - #1900 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / HORMA domain superfamily ...Helix Hairpins - #1900 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / HORMA domain superfamily / Helix Hairpins / Helix non-globular / Special / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase ATG1 / Autophagy-related protein 13
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsFujioka, Y. / Noda, N.N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25111004 Japan
Japan Science and Technology Japan
Japan Society for the Promotion of Science (JSPS)2440279 Japan
Japan Society for the Promotion of Science (JSPS)24113725 Japan
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis of starvation-induced assembly of the autophagy initiation complex.
Authors: Fujioka, Y. / Suzuki, S.W. / Yamamoto, H. / Kondo-Kakuta, C. / Kimura, Y. / Hirano, H. / Akada, R. / Inagaki, F. / Ohsumi, Y. / Noda, N.N.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Data collection
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Dec 24, 2014Group: Database references
Revision 2.0Jan 8, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site_anisotrop / entity_src_gen ...atom_site_anisotrop / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords / symmetry
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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: Atg1 tMIT
B: Atg1 tMIT
C: Atg13 MIM
D: Atg13 MIM


Theoretical massNumber of molelcules
Total (without water)75,9904
Polymers75,9904
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-78 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.995, 96.622, 63.330
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA568 - 8287 - 267
21ASPASPLEULEUBB568 - 8287 - 267
12LEULEUSERSERCC446 - 4967 - 57
22LEULEUSERSERDD446 - 4967 - 57

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.993936, -0.101644, 0.041953), (-0.109893, 0.931679, -0.346262), (-0.003891, -0.348772, -0.937199)80.93446, 26.36886, 117.06797
3given(1), (1), (1)
4given(-0.991427, -0.12217, 0.04633), (-0.130659, 0.927691, -0.349739), (-0.000253, -0.352794, -0.935701)80.65544, 27.24683, 116.8625

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Components

#1: Protein Atg1 tMIT


Mass: 31063.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Gene: ATG1 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W0T9X4*PLUS
#2: Protein Atg13 MIM


Mass: 6931.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W0TA43*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 12% PEG 3350, 0.2M ammonium acetate, 0.1M acetate buffer
PH range: 4.8

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.0, 0.9791, 0.9794, 0.964
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97941
40.9641
ReflectionResolution: 2.2→50 Å / Num. obs: 31856 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Biso Wilson estimate: 44.08 Å2 / Rsym value: 0.109 / Net I/av σ(I): 29.7 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→45.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.707 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25493 3140 9.9 %RANDOM
Rwork0.20883 ---
obs0.21333 28695 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.3 Å2 / Biso mean: 66.01 Å2 / Biso min: 24 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-1.52 Å2
2---0.49 Å20 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.2→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 0 26 3900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023928
X-RAY DIFFRACTIONr_bond_other_d0.0010.023742
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9865298
X-RAY DIFFRACTIONr_angle_other_deg0.80138622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66325.478157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36215732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5461513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02813
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_it2.1283.5091976
X-RAY DIFFRACTIONr_mcbond_other2.1283.5071975
X-RAY DIFFRACTIONr_mcangle_it3.3235.2262449
X-RAY DIFFRACTIONr_mcangle_other3.3235.2282450
X-RAY DIFFRACTIONr_scbond_it2.7443.7341952
X-RAY DIFFRACTIONr_scbond_other2.7433.7341952
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2415.4932850
X-RAY DIFFRACTIONr_long_range_B_refined6.28927.174526
X-RAY DIFFRACTIONr_long_range_B_other6.27927.1484520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1080MEDIUM POSITIONAL0.640.5
1A1612LOOSE POSITIONAL0.845
1A1080MEDIUM THERMAL7.552
1A1612LOOSE THERMAL6.2110
2C256MEDIUM POSITIONAL0.490.5
2C378LOOSE POSITIONAL0.815
2C256MEDIUM THERMAL7.592
2C378LOOSE THERMAL7.1810
LS refinement shellResolution: 2.2→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 234 -
Rwork0.226 2013 -
obs--94.61 %
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)
11.70671.68650.91233.55221.62573.64530.2227-0.2741-0.02220.663-0.2814-0.1610.17150.18190.05880.1769-0.0503-0.07310.2129-0.03770.169550.337435.904967.0054
23.1729-0.79460.02043.15970.66821.85140.01860.06970.0053-0.2702-0.28770.2580.0941-0.24480.26910.0914-0.01170.00570.09670.00330.115829.17527.848741.8268
31.63090.80620.61173.94441.0855.1418-0.0859-0.05970.09070.14560.0609-0.3423-0.46810.58350.02490.0658-0.0284-0.01950.3158-0.0350.291152.09234.487562.3123
44.9165-0.90070.87953.72140.09063.49540.06210.03650.1004-0.4701-0.15810.4786-0.1318-0.65250.0960.08640.0327-0.01490.1754-0.02410.193823.59629.065242.3249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A567 - 828
2X-RAY DIFFRACTION2B568 - 836
3X-RAY DIFFRACTION3C446 - 500
4X-RAY DIFFRACTION4D444 - 496

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