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- PDB-4p1w: Crystal structure of Atg13(17BR)-Atg17-Atg29-Atg31 complex -

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Basic information

Entry
Database: PDB / ID: 4p1w
TitleCrystal structure of Atg13(17BR)-Atg17-Atg29-Atg31 complex
Components
  • Atg13 17BR
  • Atg17
  • Atg29
  • Atg31
KeywordsPROTEIN TRANSPORT / Complex
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 / autophagosome assembly / mitophagy / autophagy / protein transport / 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: 3.2 Å
AuthorsFujioka, Y. / Noda, N.N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25111004 Japan
Japan Society for the Promotion of Science (JSPS)24113725 Japan
Japan Society for the Promotion of Science (JSPS)2440279 Japan
Japan Science and Technology 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 2.0Jan 8, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / 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_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif / 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_entity_src_syn.pdbx_alt_source_flag / _pdbx_entity_src_syn.strain / _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 / _struct_ref_seq_dif.pdbx_ordinal / _symmetry.Int_Tables_number
Revision 2.1Sep 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 / pdbx_initial_refinement_model / 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 / _diffrn_radiation_wavelength.wavelength / _refine.pdbx_diffrn_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atg29
B: Atg31
C: Atg17
D: Atg29
E: Atg31
F: Atg17
G: Atg13 17BR


Theoretical massNumber of molelcules
Total (without water)148,4207
Polymers148,4207
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-131 kcal/mol
Surface area65560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.348, 63.989, 184.600
Angle α, β, γ (deg.)90.00, 109.25, 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: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETUNKUNKAA1 - 801 - 72
21METMETUNKUNKDD1 - 801 - 72
12VALVALHISHISBB9 - 1469 - 146
22VALVALHISHISEE9 - 1469 - 146
13GLUGLUVALVALCC3 - 4133 - 413
23GLUGLUVALVALFF3 - 4133 - 413

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.184357, 0.03621, 0.982192), (0.012573, -0.999326, 0.034482), (0.982779, 0.005992, -0.184688)-146.11906, 10.05077, 164.68086
3given(1), (1), (1)
4given(0.203793, 0.027896, 0.978616), (0.011112, -0.999596, 0.02618), (0.978951, 0.005539, -0.204021)-143.06944, 11.56133, 167.79596
5given(1), (1), (1)
6given(0.243241, -0.021283, 0.969732), (-0.033847, -0.999337, -0.013443), (0.969375, -0.029553, -0.2438)-135.83395, 12.86959, 173.97768

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Components

#1: Protein Atg29 / KLTH0C07942p


Mass: 7722.015 Da / Num. of mol.: 2 / Fragment: UNP residues 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0D11660g / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5DF24
#2: Protein Atg31 / KLTH0D11660p


Mass: 17387.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0C07942g / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5DEB9
#3: Protein Atg17 / KLTH0D15642p


Mass: 48312.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0D15642g / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: C5DFJ6
#4: Protein/peptide Atg13 17BR / KLTH0A00704p


Mass: 1575.774 Da / Num. of mol.: 1 / Fragment: UNP residues 392-404 / Source method: obtained synthetically / Source: (synth.) Lachancea thermotolerans (fungus) / References: UniProt: C5DB94
Has protein modificationN
Sequence detailsThe crystallized sequence for chains A and D is ...The crystallized sequence for chains A and D is MNSENTIVYVRVAGRARNGFVDPLKFYWDLERDRSLWSSVSKLDNTKKTIDWKRLSREFKAPEHFIRKRSYALFAKHLKLLERQIE, the C-terminal fragment is disordered, it was not possible to assign the identity to some residues, they are listed as UNK residues in the sequence and coordinates.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.33 Å3/Da / Density % sol: 76.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% PEGMME 5000, 0.1M TrisHCl / PH range: 8

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 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: 54575 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.108 / Net I/av σ(I): 20.3 / Net I/σ(I): 8.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hpq

4hpq


Resolution: 3.2→44.26 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / SU B: 47.428 / SU ML: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.905 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29251 4975 10.1 %RANDOM
Rwork0.25693 ---
obs0.26058 44114 89.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 92.403 Å2
Baniso -1Baniso -2Baniso -3
1-4.95 Å20 Å25.27 Å2
2--1.68 Å20 Å2
3----6.81 Å2
Refinement stepCycle: 1 / Resolution: 3.2→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 0 0 8904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199028
X-RAY DIFFRACTIONr_bond_other_d0.0020.028514
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.94912275
X-RAY DIFFRACTIONr_angle_other_deg0.827319406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69151176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85425.47415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.159151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6171542
X-RAY DIFFRACTIONr_chiral_restr0.0710.21462
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022042
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_it5.4929.3594755
X-RAY DIFFRACTIONr_mcbond_other5.4929.3584754
X-RAY DIFFRACTIONr_mcangle_it8.79914.0265914
X-RAY DIFFRACTIONr_mcangle_other8.79814.0275915
X-RAY DIFFRACTIONr_scbond_it5.6259.4684273
X-RAY DIFFRACTIONr_scbond_other5.6249.4694274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.21914.0896362
X-RAY DIFFRACTIONr_long_range_B_refined12.76173.17710374
X-RAY DIFFRACTIONr_long_range_B_other12.76173.18310375
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
1A297MEDIUM POSITIONAL0.330.5
1A297MEDIUM THERMAL62
2B1634MEDIUM POSITIONAL0.360.5
2B1634MEDIUM THERMAL8.612
3C5221MEDIUM POSITIONAL0.630.5
3C5221MEDIUM THERMAL10.322
LS refinement shellResolution: 3.2→3.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 268 -
Rwork0.44 2568 -
obs--72.11 %
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)
11.5777-0.62140.93743.265-1.26110.8325-0.2824-0.19960.25620.47590.18970.1316-0.318-0.11240.09270.2583-0.06820.04680.14630.00710.275213.303723.337820.0661
20.17480.1625-0.33851.9977-0.86171.0901-0.0575-0.091-0.00410.0165-0.0775-0.1455-0.11990.1070.1350.28110.05390.05750.0626-0.03210.16278.09319.295514.7288
30.0565-0.01220.04510.1563-0.04660.2018-0.0437-0.0153-0.0031-0.015-0.0672-0.01010.07130.05290.11090.1630.01410.11260.07320.0180.1032-8.5591-2.852132.5343
43.63610.21920.01512.6252-0.08650.10470.0109-0.0276-0.01-0.20780.1458-0.1629-0.01710.1207-0.15670.3024-0.0085-0.00580.45320.06530.5117-111.2712-8.2562183.2314
51.07850.407-1.19891.7804-1.19342.21470.1139-0.1694-0.24060.0417-0.1129-0.04290.03140.1694-0.0010.1433-0.08010.06540.1485-0.05430.4442-119.56325.8953179.3538
60.51170.0555-0.22470.1990.01810.24930.1857-0.22670.25710.02070.0060.0885-0.12470.143-0.19160.1426-0.02520.17840.2021-0.05290.2552-103.22518.2123155.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 82
2X-RAY DIFFRACTION2B9 - 146
3X-RAY DIFFRACTION3C2 - 413
4X-RAY DIFFRACTION4D1 - 80
5X-RAY DIFFRACTION5E9 - 146
6X-RAY DIFFRACTION6F2 - 413

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