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- PDB-6kyb: Crystal structure of Atg18 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6kyb
TitleCrystal structure of Atg18 from Saccharomyces cerevisiae
ComponentsAutophagy-related protein 18
KeywordsLIPID BINDING PROTEIN / TRANSPORT PROTEIN / Macroautophagy / Atg18 / Atg2 / PROPPINs / WD40 / PI3P
Function / homology
Function and homology information


regulation of phosphatidylinositol biosynthetic process / PAS complex / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phagophore / positive regulation of vacuole organization / vacuolar protein processing / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy ...regulation of phosphatidylinositol biosynthetic process / PAS complex / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phagophore / positive regulation of vacuole organization / vacuolar protein processing / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / pexophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / phagophore assembly site / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / fungal-type vacuole membrane / vacuolar membrane / extrinsic component of membrane / autophagosome assembly / ubiquitin binding / cell periphery / macroautophagy / endosome membrane / endosome / protein-containing complex / cytosol
Similarity search - Function
: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsTang, D. / Lei, Y. / Liao, G. / Chen, Q. / Xu, L. / Lu, K. / Qi, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0506300 China
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: The crystal structure of Atg18 reveals a new binding site for Atg2 in Saccharomyces cerevisiae.
Authors: Lei, Y. / Tang, D. / Liao, G. / Xu, L. / Liu, S. / Chen, Q. / Li, C. / Duan, J. / Wang, K. / Wang, J. / Sun, B. / Li, Z. / Dai, L. / Cheng, W. / Qi, S. / Lu, K.
History
DepositionSep 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
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 18
B: Autophagy-related protein 18
C: Autophagy-related protein 18
D: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)222,2464
Polymers222,2464
Non-polymers00
Water724
1
A: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)55,5611
Polymers55,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)55,5611
Polymers55,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)55,5611
Polymers55,5611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)55,5611
Polymers55,5611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.330, 95.330, 300.871
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 25 or resid 27...
21(chain B and (resid 5 through 25 or resid 27...
31(chain C and (resid 5 through 25 or resid 27...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 25 or resid 27...A5 - 25
121(chain A and (resid 5 through 25 or resid 27...A27 - 63
131(chain A and (resid 5 through 25 or resid 27...A65
141(chain A and (resid 5 through 25 or resid 27...A6
151(chain A and (resid 5 through 25 or resid 27...A5 - 499
161(chain A and (resid 5 through 25 or resid 27...A75
171(chain A and (resid 5 through 25 or resid 27...A77 - 81
181(chain A and (resid 5 through 25 or resid 27...A5 - 499
191(chain A and (resid 5 through 25 or resid 27...A417 - 43
1101(chain A and (resid 5 through 25 or resid 27...A411 - 415
1111(chain A and (resid 5 through 25 or resid 27...A417 - 434
1121(chain A and (resid 5 through 25 or resid 27...A437 - 438
1131(chain A and (resid 5 through 25 or resid 27...A442
1141(chain A and (resid 5 through 25 or resid 27...A464 - 484
1151(chain A and (resid 5 through 25 or resid 27...A486 - 494
1161(chain A and (resid 5 through 25 or resid 27...A496 - 498
211(chain B and (resid 5 through 25 or resid 27...B5 - 25
221(chain B and (resid 5 through 25 or resid 27...B27 - 63
231(chain B and (resid 5 through 25 or resid 27...B65
241(chain B and (resid 5 through 25 or resid 27...B0
251(chain B and (resid 5 through 25 or resid 27...B77 - 81
261(chain B and (resid 5 through 25 or resid 27...B75
271(chain B and (resid 5 through 25 or resid 27...B83 - 120120
281(chain B and (resid 5 through 25 or resid 27...B5 - 498
291(chain B and (resid 5 through 25 or resid 27...B290 - 320
2101(chain B and (resid 5 through 25 or resid 27...B290 - 320
2111(chain B and (resid 5 through 25 or resid 27...B411 - 415
2121(chain B and (resid 5 through 25 or resid 27...B437 - 438
2131(chain B and (resid 5 through 25 or resid 27...B464 - 484
2141(chain B and (resid 5 through 25 or resid 27...B486 - 494
2151(chain B and (resid 5 through 25 or resid 27...B496 - 498
311(chain C and (resid 5 through 25 or resid 27...C5 - 25
321(chain C and (resid 5 through 25 or resid 27...C27 - 63
331(chain C and (resid 5 through 25 or resid 27...C65
341(chain C and (resid 5 through 25 or resid 27...C69
351(chain C and (resid 5 through 25 or resid 27...C72
361(chain C and (resid 5 through 25 or resid 27...C75
371(chain C and (resid 5 through 25 or resid 27...C77 - 81
381(chain C and (resid 5 through 25 or resid 27...C1 - 499
391(chain C and (resid 5 through 25 or resid 27...C417 - 43
3101(chain C and (resid 5 through 25 or resid 27...C411 - 415
3111(chain C and (resid 5 through 25 or resid 27...C417 - 434
3121(chain C and (resid 5 through 25 or resid 27...C437 - 438
3131(chain C and (resid 5 through 25 or resid 27...C442
3141(chain C and (resid 5 through 25 or resid 27...C464 - 484
3151(chain C and (resid 5 through 25 or resid 27...C486 - 494
3161(chain C and (resid 5 through 25 or resid 27...C496 - 498

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Components

#1: Protein
Autophagy-related protein 18 / Atg18 / Cytoplasm to vacuole targeting protein 18 / Needed for premeiotic replication protein 1 / ...Atg18 / Cytoplasm to vacuole targeting protein 18 / Needed for premeiotic replication protein 1 / Swollen vacuole phenotype protein 1


Mass: 55561.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ATG18, AUT10, CVT18, NMR1, SVP1, YFR021W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43601
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.79 Å3/Da / Density % sol: 31.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes7.5, 10%PEG6000, 5%MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 39054 / % possible obs: 98.3 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.043 / Rrim(I) all: 0.163 / Χ2: 1.779 / Net I/σ(I): 4.8 / Num. measured all: 578363
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7513.41.70619060.70.4621.770.52297
2.75-2.814.41.33219380.8080.3421.3770.53897.1
2.8-2.8515.11.20519480.8610.3051.2450.54796.8
2.85-2.9115.40.98718780.8880.2491.0190.57196.9
2.91-2.9715.20.74519370.9220.1890.7690.60197.6
2.97-3.04150.56819560.9460.1460.5870.65297.8
3.04-3.1215.10.48819350.960.1260.5040.71497.5
3.12-3.214.90.37718990.9670.0990.390.85197.1
3.2-3.314.40.3319410.9720.0890.3420.95398.2
3.3-3.413.80.27719480.9780.0760.2881.29597.5
3.4-3.5215.10.23219470.9730.0610.241.55798.6
3.52-3.6615.40.21819530.9750.0580.2261.77198.5
3.66-3.8315.20.18419640.980.0490.191.91498.6
3.83-4.0315.20.1619570.9850.0430.1662.24698.7
4.03-4.2914.50.14620060.9840.0410.1522.81799.3
4.29-4.6214.20.12919450.9840.0360.1353.22499.1
4.62-5.0815.60.12319740.9830.0330.1283.16499.1
5.08-5.8115.20.12220040.9850.0340.1272.64899.8
5.81-7.3214.40.11719860.9790.0330.1222.91399.8
7.32-5014.90.11320320.9830.0330.1195.60999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.16 Å49.85 Å
Translation3.16 Å49.85 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EXV

4exv


Resolution: 2.8→48.628 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 32.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1873 5.02 %
Rwork0.2141 35403 -
obs0.2168 37276 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.37 Å2 / Biso mean: 103.3867 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.8→48.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9868 0 0 4 9872
Biso mean---60.25 -
Num. residues----1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710070
X-RAY DIFFRACTIONf_angle_d1.29513653
X-RAY DIFFRACTIONf_chiral_restr0.0691622
X-RAY DIFFRACTIONf_plane_restr0.0071721
X-RAY DIFFRACTIONf_dihedral_angle_d10.086071
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3751X-RAY DIFFRACTION18.455TORSIONAL
12B3751X-RAY DIFFRACTION18.455TORSIONAL
13C3751X-RAY DIFFRACTION18.455TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.87580.37971540.2921265498
2.8758-2.96040.37561170.2945271597
2.9604-3.05590.38981180.2907271797
3.0559-3.16510.38311560.2941269498
3.1651-3.29180.36371470.269269898
3.2918-3.44160.3321890.2548265098
3.4416-3.6230.29931450.2321270999
3.623-3.84990.28161420.2262275399
3.8499-4.1470.26841120.2117278199
4.147-4.56410.26021200.1733277499
4.5641-5.22380.18481460.1565272799
5.2238-6.57890.2551660.22062751100
6.5789-48.6280.23751610.2082780100
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)
15.3789-2.21.25665.176-2.05694.6476-0.2644-1.3098-0.02940.54630.22270.8553-0.0768-0.8270.02770.582-0.0250.06481.0677-0.10960.7558-55.030523.24755.5721
26.4951-1.46841.20445.4755-0.25816.0159-0.2065-0.4314-0.31610.36020.35840.37080.5099-0.4813-0.18360.60030.15230.03620.82820.03340.555-40.966512.99513.8936
32.17820.95831.89155.66810.49715.3088-0.18540.31490.2031-0.0419-0.02690.0547-0.7065-0.36280.26530.71180.02940.01430.4878-0.06510.5081-33.572919.5321-4.1726
44.8039-1.58790.82383.9386-2.15313.25-0.06160.0049-0.0356-0.30210.1378-0.4722-0.11880.2574-0.06230.58880.0187-0.01860.4813-0.05250.408-34.228518.3635-10.2581
54.86261.50870.46732.33951.19974.4841-0.11110.28110.5625-0.3875-0.19280.2761-0.1037-0.06860.09660.58670.1226-0.07030.50490.0580.6242-34.944829.7818-15.27
64.7653-2.0919-3.50222.13980.14459.38870.2630.45160.6956-1.1089-0.6371-0.995-0.45350.50070.23230.5677-0.01490.07560.59570.17320.7265-43.698733.6991-18.7249
75.31590.68561.35072.56081.67255.9063-0.6479-0.40651.588-0.4972-0.5399-0.0867-0.8085-0.95411.42360.6392-0.0782-0.27760.9366-0.17931.4103-52.653537.5441-11.0351
84.32951.36083.56223.08294.20386.5212-0.49410.63521.5229-0.4881-0.75560.7666-1.1527-0.5771.43010.59460.0953-0.15680.6856-0.05221.1653-59.780136.5213-20.8288
99.1143-2.2438-4.02777.13142.91325.30361.00230.58151.4028-0.1455-0.4483-0.3656-0.7437-0.6798-0.64760.63020.1185-0.15170.6129-0.04570.9686-56.277638.2991-12.6194
105.7035-1.7466-0.66643.16060.56492.2191-0.1384-0.8368-0.09520.58260.2165-0.19550.13760.1546-0.10160.85680.0116-0.1180.6399-0.00270.3745-8.4850.305710.359
112.46633.8176-1.70356.3817-1.75933.86710.25010.09060.29820.2512-0.10230.3166-0.0880.2769-0.16010.67370.0754-0.08410.35310.010.4241-21.55933.4239-4.2972
123.0194-1.0224-0.05583.00730.98582.4080.20610.29710.0196-0.2852-0.11650.0094-0.161-0.0041-0.06940.56750.0338-0.04080.47750.00380.303-14.4546-0.4415-12.5749
135.41860.7122-0.2934.0849-0.0523.85280.15480.7837-0.5497-0.1023-0.1226-0.31060.20210.0818-0.02350.61330.1069-0.10210.6499-0.13690.45082.7179-11.7732-11.8496
140.3647-1.1782-0.36614.9397-0.35072.38370.06750.5141-1.74421.0606-0.3158-0.4057-0.031-1.1715-0.1030.76750.0523-0.36580.9747-0.21651.159114.105-35.33028.0462
154.08173.04312.90344.8242.00443.89910.7359-0.9003-1.32991.3766-0.7243-0.61810.1402-0.02330.13321.4086-0.0796-0.53520.77920.12881.395817.4301-38.078913.3821
167.3058-2.94090.00014.7862-2.6944.0085-0.1582-0.8763-0.61912.9442-0.32440.5488-0.6704-0.77570.59551.2034-0.0071-0.15841.0812-0.07760.99314.9342-33.234326.1034
178.436-3.06910.41063.90820.4754.52690.2634-1.59160.49681.0687-0.1758-0.81260.2134-0.3946-0.10321.3191-0.2015-0.5080.8813-0.03781.010324.7828-21.485622.2277
181.1271.0751-1.73316.0484-2.92337.07110.1867-0.56420.22310.8686-1.0108-0.7304-0.61880.27760.73291.2992-0.1506-0.55180.8801-0.05461.07429.3198-10.463316.6101
196.16411.62-0.53056.94161.21387.2095-0.6207-0.16461.5910.04840.2372-1.5208-0.60551.08370.59090.6953-0.0414-0.35210.8161-0.03041.21329.4681-12.71144.6453
203.09261.34180.92715.33031.7965.48580.0462-0.0814-0.5582-0.2270.1389-0.73060.36180.2881-0.22770.663-0.0047-0.19240.632-0.00180.864521.9185-26.9486-5.4079
216.62710.6239-2.84765.7710.93588.7885-0.96770.967-1.3937-0.1967-0.4196-1.33670.4119-0.62451.32680.78220.1774-0.10020.492-0.08651.095721.0756-33.7054-8.46
225.03543.14950.8086.96550.15163.5041-0.205-1.6492-0.17261.37440.08280.8074-1.5423-0.36870.18281.70310.32510.45671.02340.0450.820722.255458.75021.4863
232.4694-0.99951.96224.8862-3.43337.4699-0.1089-1.4461-0.14931.51930.19720.10630.1993-1.0568-0.03721.86460.20960.68561.65920.48410.969417.221353.69239.6008
240.7647-0.1332-0.02842.3171-1.70011.2513-0.3328-0.688-0.22931.11440.31530.46070.153-0.5896-0.27971.61220.65961.31021.58480.08550.847712.810451.684116.1643
252.57530.8260.34544.30571.38753.11950.4082-1.1311-0.60861.667-0.30171.66310.803-0.63290.10861.3151-0.26640.45431.65040.62431.71397.708338.36545.0476
264.3731.5172-0.30256.7195-0.77314.8253-0.0522-0.0546-0.64450.37920.27791.04140.0933-0.3469-0.20360.5382-0.01160.04960.6018-0.0190.812118.107647.2871-14.5532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 90 )A5 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 128 )A91 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 224 )A129 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 264 )A225 - 264
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 298 )A265 - 298
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 416 )A299 - 416
7X-RAY DIFFRACTION7chain 'A' and (resid 417 through 438 )A417 - 438
8X-RAY DIFFRACTION8chain 'A' and (resid 439 through 471 )A439 - 471
9X-RAY DIFFRACTION9chain 'A' and (resid 472 through 499 )A472 - 499
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 128 )B5 - 128
11X-RAY DIFFRACTION11chain 'B' and (resid 129 through 224 )B129 - 224
12X-RAY DIFFRACTION12chain 'B' and (resid 225 through 318 )B225 - 318
13X-RAY DIFFRACTION13chain 'B' and (resid 319 through 498 )B319 - 498
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 24 )C1 - 24
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 63 )C25 - 63
16X-RAY DIFFRACTION16chain 'C' and (resid 64 through 94 )C64 - 94
17X-RAY DIFFRACTION17chain 'C' and (resid 95 through 146 )C95 - 146
18X-RAY DIFFRACTION18chain 'C' and (resid 147 through 244 )C147 - 244
19X-RAY DIFFRACTION19chain 'C' and (resid 245 through 285 )C245 - 285
20X-RAY DIFFRACTION20chain 'C' and (resid 286 through 481 )C286 - 481
21X-RAY DIFFRACTION21chain 'C' and (resid 482 through 499 )C482 - 499
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 41 )D1 - 41
23X-RAY DIFFRACTION23chain 'D' and (resid 42 through 75 )D42 - 75
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 93 )D76 - 93
25X-RAY DIFFRACTION25chain 'D' and (resid 94 through 236 )D94 - 236
26X-RAY DIFFRACTION26chain 'D' and (resid 237 through 500 )D237 - 500

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