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- PDB-8do8: Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORM... -

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Basic information

Entry
Database: PDB / ID: 8do8
TitleCrystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer
Components
  • Autophagy-related protein 101
  • Autophagy-related protein 13
KeywordsSIGNALING PROTEIN / HORMA
Function / homology
Function and homology information


regulation of protein lipidation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / positive regulation of protein targeting to mitochondrion / Macroautophagy ...regulation of protein lipidation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / positive regulation of protein targeting to mitochondrion / Macroautophagy / mitophagy / autophagosome assembly / autophagosome / positive regulation of autophagy / protein serine/threonine kinase activator activity / negative regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 101 / Autophagy-related protein 101 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / HORMA domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 13 / Autophagy-related protein 101
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsBuffalo, C.Z. / Ren, X. / Yokom, A.L. / Hurley, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateASAP-000350 United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation.
Authors: Ren, X. / Nguyen, T.N. / Lam, W.K. / Buffalo, C.Z. / Lazarou, M. / Yokom, A.L. / Hurley, J.H.
History
DepositionJul 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 101
B: Autophagy-related protein 13
C: Autophagy-related protein 101
D: Autophagy-related protein 13
E: Autophagy-related protein 101
F: Autophagy-related protein 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,39844
Polymers143,8986
Non-polymers3,50038
Water3,369187
1
C: Autophagy-related protein 101
D: Autophagy-related protein 13
F: Autophagy-related protein 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,42319
Polymers71,9493
Non-polymers1,47416
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-22 kcal/mol
Surface area16830 Å2
MethodPISA
2
A: Autophagy-related protein 101
B: Autophagy-related protein 13
E: Autophagy-related protein 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,97525
Polymers71,9493
Non-polymers2,02622
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-21 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.453, 139.860, 147.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Autophagy-related protein 101 /


Mass: 24926.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG101, C12orf44, PP894 / Production host: Homo sapiens (human) / References: UniProt: Q9BSB4
#2: Protein Autophagy-related protein 13 /


Mass: 22096.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Homo sapiens (human) / References: UniProt: O75143
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.63 Å3/Da / Density % sol: 24.54 %
Crystal growTemperature: 273 K / Method: vapor diffusion / Details: 0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→39.41 Å / Num. obs: 37256 / % possible obs: 99.75 % / Redundancy: 6.6 % / Biso Wilson estimate: 66.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09486 / Net I/σ(I): 14.55
Reflection shellResolution: 2.41→2.496 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.279 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 3659 / CC1/2: 0.559 / CC star: 0.847 / Rpim(I) all: 0.5303 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C50

5c50


Resolution: 2.41→39.41 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1152 3.09 %
Rwork0.2039 36092 -
obs0.2054 37244 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.58 Å2 / Biso mean: 66.7164 Å2 / Biso min: 32.98 Å2
Refinement stepCycle: final / Resolution: 2.41→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 228 187 6240
Biso mean--83.02 64.87 -
Num. residues----771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.41-2.520.32981400.280944474587
2.52-2.650.28781390.246144214560
2.65-2.820.28071450.241644674612
2.82-3.040.31881450.226144634608
3.04-3.340.2411390.199944644603
3.34-3.820.281430.192145164659
3.82-4.820.22691480.172845434691
4.82-39.410.22391530.210347714924
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)
14.2393-1.24570.16615.27-1.10633.37740.18230.2855-0.277-0.57520.16230.29920.1128-0.0237-0.31410.3614-0.0679-0.03890.3019-0.0060.3907-5.2316-35.457125.5007
28.20774.9395-1.23764.55-0.1522.266-0.46070.36471.6205-1.15370.43140.3436-0.13670.00410.03660.88430.0533-0.03890.4454-0.03980.5213-3.6754-67.729823.5129
33.28310.11610.85275.36590.27062.88760.0456-0.1106-0.6594-0.33820.3110.74840.2751-0.1894-0.34460.4271-0.0753-0.06610.40390.07990.5461-7.9833-39.794329.1009
43.613-0.7246-0.23413.77380.01933.9718-0.1615-0.176-0.06680.13810.2339-1.03350.19810.3755-0.08110.2767-0.018-0.00530.3658-0.08850.56049.5307-33.104543.412
54.52781.08350.45644.17130.19842.8324-0.4164-0.04980.04430.59840.4377-1.0035-0.1521.34010.02630.4140.0184-0.19210.6155-0.08140.745112.4379-30.76345.1246
61.80590.10230.10917.1566-0.11111.6011-0.0092-0.47690.05511.16860.17730.4409-0.0451-0.1293-0.17650.57150.02920.06740.4461-0.04020.4486-1.9646-20.62851.6772
74.3862-0.38552.76015.21832.96133.80780.11832.62550.25220.45060.1599-1.01750.75241.6665-0.20630.85670.06980.22261.32570.21011.06134.9804-49.693449.6452
83.6002-2.71980.42894.1478-2.2733.82510.36240.0053-0.696-0.5342-0.10250.26340.6447-0.1466-0.2060.461-0.0605-0.01890.2159-0.03830.50461.5831-36.514640.233
98.45315.10781.93753.94683.46186.4755-0.52350.12140.903-1.2719-0.0251.0093-0.9628-0.38970.42690.57540.0750.04310.3903-0.00240.5289-4.6324-14.321538.7059
103.04810.96740.32282.70160.39850.77430.1517-0.55650.40980.6865-0.00990.13390.1562-0.1108-0.18050.5330.04440.02650.4943-0.11170.3917-3.0081-20.290153.6619
119.2188-4.360.87472.7191-0.11352.7258-0.2137-0.4309-0.05031.00590.30110.76150.0799-0.2698-0.04850.4192-0.0260.06810.433-0.02520.3938-6.5772-29.325249.1139
122.7148-0.6877-0.75112.39850.5054.6838-0.13650.0875-0.34320.2023-0.0490.14280.711-0.45940.09680.5148-0.1760.03320.4906-0.1170.4235-5.111-75.439663.0079
130.69440.8726-0.21831.06040.90513.40170.0559-0.009-0.1582-0.07520.0305-0.24920.07680.7339-0.09820.46540.01510.04780.4673-0.05540.42561.882-73.269250.1825
146.9613-3.71680.95168.9782-1.46347.731-0.679-0.33810.67720.68650.5-1.11540.32460.9617-0.03480.51040.06290.08280.7373-0.14880.57013.7708-69.054272.074
156.4869-1.7190.66573.6833-0.95844.73930.22010.97090.2280.091-0.46970.17490.6113-1.04260.09790.6526-0.1913-0.02320.698-0.1520.4151-8.4681-70.295351.4284
163.0709-0.3882-0.47741.49340.46854.2350.05640.2157-0.1539-0.2045-0.05950.38540.0985-1.673-0.05320.4060.02340.01880.8978-0.05890.4008-20.3136-60.810969.7733
175.071.2623-0.55327.40590.4017.8331-0.0993-0.62730.2968-0.25260.01961.0592-1.4264-1.35730.14780.60750.22270.09380.8353-0.02190.5697-20.6699-50.168779.3378
181.4815-0.5310.69272.4873-1.85888.8931-0.1019-0.03710.0750.19430.0127-0.0736-0.9297-0.31010.06560.372-0.02540.0250.4201-0.04690.3988-10.1089-56.189174.59
196.3362-0.2084-3.64764.8341-1.39882.6579-0.464-0.2655-0.95580.2176-0.2060.04671.50170.62750.70860.56120.0578-0.00810.4634-0.06430.4431-5.945-70.803485.878
204.1377-1.2140.26290.8289-0.78093.22180.317-0.22250.78370.1656-0.3331-0.1354-0.5985-0.2896-0.00290.65350.0255-0.0460.454-0.12850.431-7.5338-54.352786.9213
216.5485-2.23861.65724.0345-0.42183.2924-0.14360.04580.1711-0.01750.0421-0.17-0.95190.28750.26230.3923-0.05690.0030.3374-0.07730.3497-3.5898-54.340974.7346
224.31050.6408-0.6895.68880.49824.530.0681-0.741.08050.18510.239-0.2537-0.4282-0.1196-0.35380.63710.20970.0270.7886-0.22720.723617.0122-43.242839.8315
233.4367-0.00013.88565.31191.00724.68340.4134-1.36730.134-0.0223-0.61470.10330.7337-0.6799-0.0850.5073-0.1099-0.0391.55310.00520.6392-25.9283-58.588457.4543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 106 )A3 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 114 )A107 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 195 )A115 - 195
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 42 )B5 - 42
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 78 )B43 - 78
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 104 )B79 - 104
7X-RAY DIFFRACTION7chain 'B' and (resid 105 through 115 )B105 - 115
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 133 )B116 - 133
9X-RAY DIFFRACTION9chain 'B' and (resid 134 through 147 )B134 - 147
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 168 )B148 - 168
11X-RAY DIFFRACTION11chain 'B' and (resid 169 through 196 )B169 - 196
12X-RAY DIFFRACTION12chain 'C' and (resid 3 through 90 )C3 - 90
13X-RAY DIFFRACTION13chain 'C' and (resid 91 through 136 )C91 - 136
14X-RAY DIFFRACTION14chain 'C' and (resid 137 through 161 )C137 - 161
15X-RAY DIFFRACTION15chain 'C' and (resid 162 through 198 )C162 - 198
16X-RAY DIFFRACTION16chain 'D' and (resid 5 through 58 )D5 - 58
17X-RAY DIFFRACTION17chain 'D' and (resid 59 through 78 )D59 - 78
18X-RAY DIFFRACTION18chain 'D' and (resid 79 through 133 )D79 - 133
19X-RAY DIFFRACTION19chain 'D' and (resid 134 through 147 )D134 - 147
20X-RAY DIFFRACTION20chain 'D' and (resid 148 through 168 )D148 - 168
21X-RAY DIFFRACTION21chain 'D' and (resid 169 through 194 )D169 - 194
22X-RAY DIFFRACTION22chain 'E' and (resid 830 through 839 )E830 - 839
23X-RAY DIFFRACTION23chain 'F' and (resid 832 through 839 )F832 - 839

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