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- PDB-5xv1: Crystal structure of ATG101-ATG13HORMA -

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Basic information

Entry
Database: PDB / ID: 5xv1
TitleCrystal structure of ATG101-ATG13HORMA
Components
  • Autophagy-related protein 101
  • Autophagy-related protein 13
KeywordsPROTEIN BINDING / AUTOPHAGY / ATG101 / ATG13 / 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 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
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: 2.508 Å
AuthorsKim, B.-W. / Song, H.K.
CitationJournal: To Be Published
Title: Crystal structure of ATG101-ATG13HORMA
Authors: Kim, B.-W. / Song, H.K.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.unpublished_flag
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 13
B: Autophagy-related protein 101
C: Autophagy-related protein 13
D: Autophagy-related protein 101


Theoretical massNumber of molelcules
Total (without water)92,3644
Polymers92,3644
Non-polymers00
Water57632
1
A: Autophagy-related protein 13
B: Autophagy-related protein 101


Theoretical massNumber of molelcules
Total (without water)46,1822
Polymers46,1822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-11 kcal/mol
Surface area19090 Å2
MethodPISA
2
C: Autophagy-related protein 13
D: Autophagy-related protein 101


Theoretical massNumber of molelcules
Total (without water)46,1822
Polymers46,1822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-12 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.483, 125.505, 101.038
Angle α, β, γ (deg.)90.000, 101.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Autophagy-related protein 13 /


Mass: 21319.652 Da / Num. of mol.: 2 / Fragment: UNP residues 1-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Escherichia coli (E. coli) / References: UniProt: O75143
#2: Protein Autophagy-related protein 101 /


Mass: 24862.424 Da / Num. of mol.: 2 / Mutation: K40A/K41A/E42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG101, C12orf44, PP894 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSB4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5084→50 Å / Num. obs: 36707 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.037 / Rrim(I) all: 0.062 / Χ2: 0.755 / Net I/av σ(I): 15.541 / Net I/σ(I): 6 / Num. measured all: 229055

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XYU

5xyu


Resolution: 2.508→32.984 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.85
RfactorNum. reflection% reflection
Rfree0.2512 1998 5.45 %
Rwork0.2105 --
obs0.2128 36673 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 224.9 Å2 / Biso mean: 78.872 Å2 / Biso min: 30.25 Å2
Refinement stepCycle: final / Resolution: 2.508→32.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 0 32 6095
Biso mean---60.22 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076165
X-RAY DIFFRACTIONf_angle_d0.9268356
X-RAY DIFFRACTIONf_chiral_restr0.051982
X-RAY DIFFRACTIONf_plane_restr0.0051060
X-RAY DIFFRACTIONf_dihedral_angle_d15.5823696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5084-2.57110.30851280.29342233236189
2.5711-2.64060.35861440.273124842628100
2.6406-2.71830.32241430.274924722615100
2.7183-2.8060.35351430.274324792622100
2.806-2.90620.3071430.26624932636100
2.9062-3.02250.32871420.249824802622100
3.0225-3.15990.31161440.244525072651100
3.1599-3.32640.26031440.244424922636100
3.3264-3.53460.29991430.234124812624100
3.5346-3.80710.24321430.207524962639100
3.8071-4.18960.22011450.191924982643100
4.1896-4.79420.20911450.172525152660100
4.7942-6.03420.22121440.191725012645100
6.0342-32.98730.21381470.177325442691100
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)
12.86660.57680.80124.2302-0.33495.7917-0.0377-0.0030.3367-0.9352-0.3085-0.06120.7526-0.0630.38620.577-0.03660.07380.46310.01810.4678-22.71756.9903225.1096
23.67322.8197-0.14884.3236-0.28815.37220.07980.9523-0.6169-1.60440.29170.98272.7664-0.00930.35411.7186-0.14490.13340.6827-0.06220.4577-26.7018-4.0639217.8115
31.6410.7023-1.24451.52240.59652.3122-0.13490.2903-0.3738-0.5733-0.13220.25582.1328-0.33060.35951.6451-0.19180.01580.6794-0.04490.7583-26.1444-12.45230.7605
41.6350.1853-0.06651.8670.43531.8599-0.3475-0.8407-1.40070.16460.46670.61011.4381-1.5653-0.40441.0513-0.2324-0.30131.3679-0.01211.3535-44.25438.4791225.144
52.37270.588-1.77352.69091.63685.1762-0.0235-0.2603-0.0317-0.1005-0.26240.22741.0174-0.0070.41720.4758-0.12620.06450.4596-0.00470.5189-24.09271.7169235.3116
61.64140.5662-0.69062.3003-0.67335.71340.2281-0.7598-1.2601-1.32710.05310.85712.6049-0.286-0.26012.0466-0.2945-0.1420.6198-0.09430.8055-28.5089-13.8137229.5066
72.1818-1.0922-0.39523.62531.15390.53560.1702-0.7437-0.62480.02580.32521.42921.6122-1.5237-0.21331.1101-0.52760.00370.9955-0.05760.7943-35.2822-1.6276233.2277
81.8730.5346-1.29363.2818-0.57274.48080.019-0.3794-0.38530.40360.04150.2891-0.3963-0.06350.01990.4479-0.1150.03590.52480.04290.4292-25.82258.1083252.1495
92.10610.0229-0.34172.3211-2.21293.0398-0.0483-0.1497-0.06110.1687-0.3969-0.511-0.22940.59980.36020.3751-0.0594-0.06190.50710.04460.4863-19.39413.7431238.3269
103.57920.1648-0.6863.8813-0.74445.76890.0543-0.7801-0.55281.3433-0.9319-0.8434-1.21811.20460.33120.9904-0.2963-0.16640.73980.1860.5946-16.075314.612257.148
113.47671.2166-1.01333.5009-0.62213.43630.0188-0.64450.02220.72460.3570.5895-0.7608-0.57160.07791.07280.06510.08810.589-0.04020.5225-29.26718.2864254.7368
120.24490.0250.09384.43633.58712.9570.7280.76330.33321.9681-1.36410.9019-2.74080.26330.07092.067-0.05360.01970.7471-0.03761.0498-35.553440.7546250.0433
131.4769-1.0018-0.84466.4209-2.92063.9622-0.2151-0.7476-0.16331.41070.68120.6053-0.9701-1.01250.16870.7661-0.04160.12040.7082-0.10910.6135-28.662411.0043256.2978
143.2506-0.35683.35275.2558-1.4857.6229-0.0226-0.7696-0.485-0.02950.15090.33520.8636-0.764-0.13320.5039-0.09470.18870.59620.06080.6162-24.5409-2.598251.8905
153.34071.003-0.70295.9857-2.12724.68260.5263-0.7140.7240.58450.3171.651-1.9474-1.3652-0.48761.31130.4150.16890.77530.07840.819-33.006925.42237.4211
162.89871.0451-0.795.3697-0.83195.98310.40940.15840.1330.686-0.3744-0.6051-0.98530.2717-0.5020.7853-0.1375-0.0010.4775-0.04470.5648-22.098822.9083239.9697
171.23060.9323-1.64311.1455-2.31946.19950.3857-0.24810.11231.3418-0.05990.2064-1.7122-0.4182-0.11071.4654-0.32490.10480.6988-0.08790.4149-25.715918.2264257.4287
181.64690.1606-1.94698.3793-1.43492.67150.8210.2020.9735-0.56050.03351.0577-0.48530.7012-1.05341.55670.0650.06350.92030.14241.1967-37.15695.5091271.132
192.00371.2383-4.22057.27893.39473.6716-0.18670.63331.7987-0.0084-0.38231.3866-3.2895-3.4591.26712.32850.3659-0.51012.5184-0.38371.2556-49.6037-7.0621270.3741
202.9767-0.70180.86892.73260.2753.6017-0.1477-0.2982-0.78110.1781-0.040.31250.1392-0.40410.05710.30110.04930.0260.49430.02090.5372-28.528945.7953221.4646
214.2793-0.3094-1.03381.5329-2.38794.48080.0720.32840.14810.8587-0.3862-2.7213-0.59621.07450.44990.5026-0.0958-0.12980.77460.14610.669-8.723746.0654216.2929
221.338-1.1343-1.38235.19980.10751.5713-0.3546-0.1102-0.57831.6384-0.1732-0.73270.260.41510.43210.6283-0.0423-0.03180.50620.07240.5225-18.175939.9157222.1283
233.2321-1.0869-2.86283.61320.21435.08280.5216-0.20380.51410.3741-0.07810.1429-1.2393-0.1962-0.30640.67540.06210.01150.5232-0.00640.5294-25.361260.0182219.5227
240.07210.09040.17570.06130.09390.7397-0.2228-1.38090.01090.10170.1350.51120.2214-1.76390.32880.7317-0.0258-0.31261.124801.471-39.717440.464213.4402
251.12780.0657-1.29572.316-1.19422.5178-0.08750.30980.0134-0.0388-0.09270.50460.1447-0.18650.23880.2320.036-0.16220.4707-0.01080.5386-24.021843.8067211.2992
261.4963-2.1395-1.86944.24330.04486.43910.6654-0.2611.3330.6457-0.2597-0.1137-1.56690.5026-0.03090.8474-0.15710.09540.48-0.05150.7818-14.85262.4449214.2544
274.30590.07630.86982.44060.32720.31870.71240.10851.1699-0.97970.13182.3574-0.6599-1.2957-0.33871.04410.26960.14790.69460.1451.3642-29.099767.6677208.9803
282.0432-0.42920.17182.72091.9361.588-0.3031.18820.6726-1.47820.31091.04890.1777-0.8899-0.19470.39090.2237-0.10910.82070.12590.709-30.777252.3354208.5003
291.62740.1318-1.37495.3254-1.86033.91840.13080.1383-0.0228-0.6265-0.2795-0.08020.32340.31390.11610.33140.1075-0.00530.47050.08030.4023-14.277439.948202.9386
301.8030.22911.13454.38620.95030.7381-0.19260.1449-0.0044-1.0832-0.1827-0.38270.40970.09480.40160.99350.08410.27370.6306-0.0020.5705-11.414630.9623192.4445
311.73340.644-0.72476.09691.46714.52450.24090.43460.1488-0.5958-0.1524-0.1455-0.1508-0.1073-0.10980.62750.1441-0.06670.52150.08020.4353-14.405748.2228193.3239
322.4836-0.3959-2.21574.0765-1.25156.7596-0.17020.3023-0.2989-0.7804-0.1733-0.05151.3992-0.42780.39810.89490.05120.05540.4824-0.06240.5957-19.795928.3191202.9545
330.29350.42960.37511.46591.21031.1517-0.6879-0.64340.32171.24060.44520.47371.3568-0.93880.34991.36390.0240.141.16940.10731.1933-25.556752.2451172.6019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 58 )A6 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 78 )A59 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 103 )A79 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 114 )A104 - 114
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 147 )A115 - 147
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 168 )A148 - 168
7X-RAY DIFFRACTION7chain 'A' and (resid 169 through 190 )A169 - 190
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 31 )B1 - 31
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 69 )B32 - 69
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 90 )B70 - 90
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 106 )B91 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 114 )B107 - 114
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 133 )B115 - 133
14X-RAY DIFFRACTION14chain 'B' and (resid 134 through 161 )B134 - 161
15X-RAY DIFFRACTION15chain 'B' and (resid 162 through 176 )B162 - 176
16X-RAY DIFFRACTION16chain 'B' and (resid 177 through 189 )B177 - 189
17X-RAY DIFFRACTION17chain 'B' and (resid 190 through 196 )B190 - 196
18X-RAY DIFFRACTION18chain 'B' and (resid 197 through 204 )B197 - 204
19X-RAY DIFFRACTION19chain 'B' and (resid 205 through 211 )B205 - 211
20X-RAY DIFFRACTION20chain 'C' and (resid 6 through 32 )C6 - 32
21X-RAY DIFFRACTION21chain 'C' and (resid 33 through 42 )C33 - 42
22X-RAY DIFFRACTION22chain 'C' and (resid 43 through 58 )C43 - 58
23X-RAY DIFFRACTION23chain 'C' and (resid 59 through 103 )C59 - 103
24X-RAY DIFFRACTION24chain 'C' and (resid 104 through 115 )C104 - 115
25X-RAY DIFFRACTION25chain 'C' and (resid 116 through 133 )C116 - 133
26X-RAY DIFFRACTION26chain 'C' and (resid 134 through 157 )C134 - 157
27X-RAY DIFFRACTION27chain 'C' and (resid 158 through 168 )C158 - 168
28X-RAY DIFFRACTION28chain 'C' and (resid 169 through 190 )C169 - 190
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 69 )D1 - 69
30X-RAY DIFFRACTION30chain 'D' and (resid 70 through 114 )D70 - 114
31X-RAY DIFFRACTION31chain 'D' and (resid 115 through 161 )D115 - 161
32X-RAY DIFFRACTION32chain 'D' and (resid 162 through 196 )D162 - 196
33X-RAY DIFFRACTION33chain 'D' and (resid 197 through 216 )D197 - 216

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