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- PDB-4hpq: Crystal Structure of the Atg17-Atg31-Atg29 Complex -

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Basic information

Entry
Database: PDB / ID: 4hpq
TitleCrystal Structure of the Atg17-Atg31-Atg29 Complex
Components
  • Atg17
  • Atg29
  • Atg31
KeywordsPROTEIN TRANSPORT / Autophagy
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / protein kinase activator activity / autophagosome assembly / autophagy / protein transport / molecular adaptor activity
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 / Mutm (Fpg) Protein; Chain: A, domain 2 / Arc Repressor Mutant, subunit A / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
KLTH0C07942p / Autophagy-related protein 29 / Autophagy-related protein 17
Similarity search - Component
Biological speciesLachancea thermotolerans CBS 6340 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.06 Å
AuthorsStanley, R.E. / Ragusa, M.J. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Architecture of the atg17 complex as a scaffold for autophagosome biogenesis.
Authors: Ragusa, M.J. / Stanley, R.E. / Hurley, J.H.
History
DepositionOct 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 10, 2018Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_gene
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)147,6476
Polymers147,6476
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16930 Å2
ΔGint-112.5 kcal/mol
Surface area67400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.370, 64.200, 184.210
Angle α, β, γ (deg.)90.00, 110.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.178807, -0.001487, 0.983883), (-0.027445, -0.999617, 0.003477), (0.983501, -0.027625, -0.17878)-33.01707, -20.25072, 31.99539

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Components

#1: Protein Atg29 / KLTH0C07942p


Mass: 7222.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans CBS 6340 (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Plasmid: pst39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5DF24
#2: Protein Atg31 / KLTH0D11660p


Mass: 18288.232 Da / Num. of mol.: 2 / Mutation: L87M, L110M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans CBS 6340 (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Plasmid: pst39 / 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 CBS 6340 (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Plasmid: pst39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5DFJ6
Sequence detailsTHE COMPLETE CRYSTALLIZED SEQUENCE OF CHAIN A AND D IS: ...THE COMPLETE CRYSTALLIZED SEQUENCE OF CHAIN A AND D IS: MNSENTIVYVRVAGRARNGFVDPLKFYWDLERDRSLWSSVSKLDNTKKTIDWKRLSREFKAPEHFIRKRSYALFAKHLKLLERQIE.THE C-TERMINAL RESIUES 51-79 ARE IN THE REGION WITH POOR ELECTRON DENSITY AND REPRESENTED AS UNKNOWN RESIDUES (UNK) IN THE COORDINATES SINCE THE SEQUENC REGISTER IS NOT KNOWN.

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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: 5.41 Å3/Da / Density % sol: 77.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Tris pH8, 4-10% peg 2KMME, 10-20% ethylene glycol, 100 mM NaCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 22-BM1
SYNCHROTRONAPS 22-ID2
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJun 4, 2012
MARMOSAIC 300 mm CCD2CCDFeb 5, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal - liquid nitrogen cooledSINGLE WAVELENGTHMx-ray1
2double crystal - liquid nitrogen cooledSINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.055→50 Å / Num. all: 59513 / Num. obs: 47730 / % possible obs: 80.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.096 / Rsym value: 0.074 / Net I/σ(I): 16
Reflection shellResolution: 3.055→3.2 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.1 / % possible all: 29

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.06→46.56 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.812 / SU B: 20.473 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R: 1.224 / ESU R Free: 0.529 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33622 2329 5.1 %RANDOM
Rwork0.30312 ---
obs0.3048 43481 75.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å21.14 Å2
2---0.55 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 3.06→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9220 0 0 0 9220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199336
X-RAY DIFFRACTIONr_bond_other_d0.0020.029012
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.95612586
X-RAY DIFFRACTIONr_angle_other_deg0.891320656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41651146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.83825.208480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.598151732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1881564
X-RAY DIFFRACTIONr_chiral_restr0.0720.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210638
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022134
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.056→3.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 25 -
Rwork0.377 586 -
obs--13.82 %

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