- PDB-4hpq: Crystal Structure of the Atg17-Atg31-Atg29 Complex -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4hpq
Title
Crystal Structure of the Atg17-Atg31-Atg29 Complex
Components
Atg17
Atg29
Atg31
Keywords
PROTEIN 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
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 details
THE 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
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 5.41 Å3/Da / Density % sol: 77.24 %
Crystal grow
Temperature: 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
Resolution: 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
Name
Version
Classification
HKL-2000
datacollection
SOLVE
phasing
REFMAC
5.7.0029
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.33622
2329
5.1 %
RANDOM
Rwork
0.30312
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obs
0.3048
43481
75.44 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 71.58 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.32 Å2
-0 Å2
1.14 Å2
2-
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-0.55 Å2
-0 Å2
3-
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-0.16 Å2
Refinement step
Cycle: LAST / Resolution: 3.06→46.56 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9220
0
0
0
9220
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.019
9336
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
9012
X-RAY DIFFRACTION
r_angle_refined_deg
1.468
1.956
12586
X-RAY DIFFRACTION
r_angle_other_deg
0.891
3
20656
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.416
5
1146
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
42.838
25.208
480
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
25.598
15
1732
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.188
15
64
X-RAY DIFFRACTION
r_chiral_restr
0.072
0.2
1448
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
10638
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
2134
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3.056→3.135 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.317
25
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Rwork
0.377
586
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obs
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13.82 %
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