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- PDB-5jge: Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide -

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Basic information

Entry
Database: PDB / ID: 5jge
TitleCrystal structure of Atg19 coiled-coil complexed with Ape1 propeptide
Components
  • Ape1 propeptide
  • Autophagy-related protein 19
KeywordsPROTEIN TRANSPORT / Receptor / Complex
Function / homology
Function and homology information


aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / vesicle organization / phagophore assembly site membrane / fungal-type vacuole / protein-containing complex localization / phagophore assembly site / metalloaminopeptidase activity / ERAD pathway ...aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / vesicle organization / phagophore assembly site membrane / fungal-type vacuole / protein-containing complex localization / phagophore assembly site / metalloaminopeptidase activity / ERAD pathway / autophagy / protein transport / protein-macromolecule adaptor activity / proteolysis / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg19/Atg34, C-terminal / Autophagy protein Atg19, Atg8-binding / Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18)
Similarity search - Domain/homology
Vacuolar aminopeptidase 1 / Autophagy-related protein 19
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsWatanabe, Y. / Noda, N.N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Agency Japan
CitationJournal: Cell Rep / Year: 2016
Title: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates
Authors: Yamasaki, A. / Watanabe, Y. / Adachi, W. / Suzuki, K. / Matoba, K. / Kirisako, H. / Kumeta, H. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F. / Noda, N.N.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Feb 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 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Autophagy-related protein 19
B: Autophagy-related protein 19
C: Ape1 propeptide
D: Autophagy-related protein 19
E: Autophagy-related protein 19
F: Ape1 propeptide


Theoretical massNumber of molelcules
Total (without water)20,7806
Polymers20,7806
Non-polymers00
Water3,171176
1
A: Autophagy-related protein 19
B: Autophagy-related protein 19
C: Ape1 propeptide


Theoretical massNumber of molelcules
Total (without water)10,3903
Polymers10,3903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-28 kcal/mol
Surface area6090 Å2
MethodPISA
2
D: Autophagy-related protein 19
E: Autophagy-related protein 19
F: Ape1 propeptide


Theoretical massNumber of molelcules
Total (without water)10,3903
Polymers10,3903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-29 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.875, 32.921, 56.957
Angle α, β, γ (deg.)87.19, 76.52, 67.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23E
14B
24E
15C
25F

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
11HISHISGLNGLNAA158 - 1813 - 26
21HISHISGLNGLNBB158 - 1813 - 26
12HISHISTHRTHRAA158 - 1843 - 29
22HISHISTHRTHRDD158 - 1843 - 29
13HISHISTHRTHRAA158 - 1843 - 29
23HISHISTHRTHREE158 - 1843 - 29
14GLYGLYGLNGLNBB156 - 1811 - 26
24GLYGLYGLNGLNEE156 - 1811 - 26
15GLYGLYTYRTYRCC-1 - 211 - 23
25GLYGLYTYRTYRFF-1 - 211 - 23

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein/peptide
Autophagy-related protein 19 / Cytoplasm-to-vacuole targeting protein 19


Mass: 3804.433 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATG19, CVT19, YOL082W, O0980, YOL01 / Production host: Escherichia coli (E. coli) / References: UniProt: P35193
#2: Protein/peptide Ape1 propeptide


Mass: 2781.269 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P14904*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 200 mM sodium acetate, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.0000, 0.9792
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
ReflectionResolution: 1.9→55.33 Å / Num. obs: 13677 / % possible obs: 97.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.458 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→55.33 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.881 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24615 686 5 %RANDOM
Rwork0.19444 ---
obs0.19698 12989 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.2 Å2-1.49 Å2
2---1.2 Å21.72 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.91→55.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 176 1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191346
X-RAY DIFFRACTIONr_bond_other_d0.0080.021399
X-RAY DIFFRACTIONr_angle_refined_deg1.6332.0311790
X-RAY DIFFRACTIONr_angle_other_deg1.77533248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7545155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.37327.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55715315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.213152
X-RAY DIFFRACTIONr_chiral_restr0.0880.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021438
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02252
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_it1.021.819638
X-RAY DIFFRACTIONr_mcbond_other1.0151.818637
X-RAY DIFFRACTIONr_mcangle_it1.6272.703787
X-RAY DIFFRACTIONr_mcangle_other1.6272.704788
X-RAY DIFFRACTIONr_scbond_it1.3171.99708
X-RAY DIFFRACTIONr_scbond_other1.3161.99708
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1662.9191003
X-RAY DIFFRACTIONr_long_range_B_refined6.88915.7991678
X-RAY DIFFRACTIONr_long_range_B_other6.57914.6911586
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)
11A20780.28
12B20780.28
21A27000.19
22D27000.19
31A23240.29
32E23240.29
41B25800.18
42E25800.18
51C23440.14
52F23440.14
LS refinement shellResolution: 1.905→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 43 -
Rwork0.257 835 -
obs--82.91 %
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)
114.0987-10.12758.635911.8775-7.91467.68590.0030.39910.1645-0.32880.008-0.09430.0257-0.1472-0.0110.1286-0.01730.02560.1759-0.02070.047728.495-4.94936.309
217.608-0.514412.10571.2672-0.565810.9057-0.0550.5807-0.1962-0.03130.0598-0.1714-0.04820.1477-0.00480.1022-0.03040.01370.0592-0.00620.134524.669-7.25946.187
311.9108-4.60673.90013.7002-2.53212.1950.03360.23770.2467-0.0207-0.08460.0319-0.00570.20830.0510.067-0.0090.02960.0871-0.02280.08231.938-0.21445.049
414.65288.0723-7.36166.9911-4.86045.4330.148-0.3806-0.00940.3481-0.08650.0417-0.1853-0.1321-0.06150.13620.0381-0.0220.1584-0.01370.039343.9757.35667.491
59.71611.153-7.0740.4417-0.40996.9902-0.1348-0.3009-0.1964-0.0683-0.0792-0.02790.0450.01130.2140.05470.0149-0.00140.05010.01350.057337.6829.06659.16
610.50135.6535-2.27584.7947-1.92291.64020.0102-0.0937-0.10590.00020.00950.1549-0.0154-0.0134-0.01970.0438-0.0073-0.02710.01160.00670.047646.3022.74258.639
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A158 - 185
2X-RAY DIFFRACTION2B156 - 182
3X-RAY DIFFRACTION3C-1 - 21
4X-RAY DIFFRACTION4D156 - 185
5X-RAY DIFFRACTION5E156 - 185
6X-RAY DIFFRACTION6F-1 - 21

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