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- PDB-5xv3: Crystal structure of ATG101-ATG13HORMA -

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Basic information

Entry
Database: PDB / ID: 5xv3
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 / autophagosome assembly / mitophagy / positive regulation of autophagy / autophagosome / protein serine/threonine kinase activator activity / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein-containing complex binding / protein kinase binding / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 101 / Autophagy-related protein 101 / 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
DI(HYDROXYETHYL)ETHER / Autophagy-related protein 13 / Autophagy-related protein 101
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsKim, B.-W. / Song, H.K.
CitationJournal: Autophagy / Year: 2018
Title: The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation.
Authors: Kim, B.-W. / Jin, Y. / Kim, J. / Kim, J.H. / Jung, J. / Kang, S. / Kim, I.Y. / Kim, J. / Cheong, H. / Song, H.K.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / 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 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4705
Polymers92,3644
Non-polymers1061
Water1,26170
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 area2790 Å2
ΔGint-11 kcal/mol
Surface area18600 Å2
MethodPISA
2
C: Autophagy-related protein 13
D: Autophagy-related protein 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2883
Polymers46,1822
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-11 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.775, 101.116, 125.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 58.5 %
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: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 36347 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 54.38 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.034 / Rrim(I) all: 0.098 / Χ2: 1.058 / Net I/av σ(I): 26.647 / Net I/σ(I): 7.5 / Num. measured all: 299829
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.57-2.618.20.88917770.9390.3270.9480.727100
2.61-2.668.30.87917940.950.3230.9370.752100
2.66-2.718.40.78217690.9380.2860.8330.829100
2.71-2.778.40.70917990.9710.2580.7550.771100
2.77-2.838.40.55218000.9680.2020.5880.744100
2.83-2.898.40.51317850.9730.1870.5460.763100
2.89-2.978.40.37317940.9880.1360.3970.772100
2.97-3.058.30.30217980.9920.1110.3220.799100
3.05-3.148.40.25418040.9920.0930.270.799100
3.14-3.248.40.19118020.9940.070.2040.813100
3.24-3.358.40.14618080.9970.0530.1550.866100
3.35-3.498.30.13218090.9970.0490.1411.05100
3.49-3.658.30.11518120.9970.0430.1231.236100
3.65-3.848.30.10118070.9970.0380.1081.509100
3.84-4.088.20.0918250.9960.0340.0961.734100
4.08-4.398.20.07718340.9980.0290.0831.932100
4.39-4.848.20.05918380.9990.0220.0631.593100
4.84-5.538.20.04618500.9990.0170.0491.133100
5.53-6.978.10.04118740.9990.0160.0441.045100
6.97-507.60.03119680.9990.0120.0341.29999.1

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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: 5XUY
Resolution: 2.57→38.593 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.63
RfactorNum. reflection% reflection
Rfree0.2826 1995 5.51 %
Rwork0.2321 --
obs0.2348 36175 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.17 Å2 / Biso mean: 82.9842 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.57→38.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5823 0 7 70 5900
Biso mean--85.15 72.37 -
Num. residues----774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045928
X-RAY DIFFRACTIONf_angle_d0.7668046
X-RAY DIFFRACTIONf_chiral_restr0.045956
X-RAY DIFFRACTIONf_plane_restr0.0041017
X-RAY DIFFRACTIONf_dihedral_angle_d16.3433532
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 (%)
2.5501-2.61380.30911250.31292135226087
2.6138-2.68450.37891400.31962395253599
2.6845-2.76350.41211420.30962422256499
2.7635-2.85260.35891420.290724392581100
2.8526-2.95460.36491420.27424242566100
2.9546-3.07280.33911420.281924332575100
3.0728-3.21260.30041440.277724612605100
3.2126-3.38190.31951430.256424512594100
3.3819-3.59360.33111430.244824522595100
3.5936-3.87090.27331430.222224532596100
3.8709-4.25990.3051440.20824712615100
4.2599-4.87530.23351450.186924972642100
4.8753-6.13840.27621480.216725232671100
6.1384-38.5970.21541520.20542624277699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.65832.0875-0.11848.745-1.19195.46190.0908-0.17420.2736-0.7451-0.00740.8523-0.62620.559-0.08340.60150.0284-0.15020.3909-0.03990.3902-16.639621.101-11.5359
29.43091.8321-1.3972-2.92234.6920.2263-0.5448-0.1951.3570.33981.10330.3384-1.1756-0.56610.6110.05010.12030.5610.15410.647-34.278811.0742-8.5819
32-0.45024.48422-3.29849.9473-0.64310.00990.65110.55880.56441.5135-1.8423-0.84330.07870.76810.11850.06160.5374-0.01190.4293-26.545919.2923-20.7317
46.16022.95922.80856.82541.19178.48240.038-0.8360.98870.169-0.01151.5473-1.4379-0.9193-0.02651.29920.19070.1060.5226-0.01940.6088-25.80423.3651-4.5606
56.88442.7062-2.4987.6225-4.317520.244-1.0425-0.3701-0.20660.13492.20740.12920.0929-0.3791.37210.0444-0.12930.6906-0.03890.5796-18.129117.82014.6392
66.0071.58252.98079.91920.40641.49420.4621-0.8004-0.1449-0.1985-0.11732.18320.47160.6615-0.34481.23440.0873-0.26440.6684-0.00120.5333-16.651911.60483.3921
72.85960.6342-1.59482.21821.76283.0456-1.17590.70791.60211.0180.9991-0.4305-0.60790.36290.17671.0786-0.2197-0.41291.19690.10961.3866-3.172514.8813-16.8228
88.56161.9833-1.38667.037-3.35362-0.19760.025-0.2319-0.49990.50360.7056-0.11160.5122-0.3060.51990.1113-0.09790.5146-0.08130.3739-18.878910.4312-13.8136
93.16050.70823.78329.53722.89814.97680.2178-0.81710.10090.92990.25682.4786-0.9604-0.2539-0.47461.58790.11270.17050.79590.07890.5644-27.709611.07744.8652
100.7930.7666-1.94080.741-1.87614.74990.6784-0.0034-0.1445-0.9683-1.21351.34870.48361.71990.53512.0692-0.093-0.28491.31740.20450.7994-13.75258.142610.782
110.8899-0.4062-0.74113.82651.56011.02710.1654-0.7705-0.4803-0.8575-0.52340.96360.12880.86280.3580.91630.0667-0.39520.66080.02360.7241-12.23928.7231-4.6737
121.83710.4197-0.5189.6129-5.73727.08760.0585-0.0588-0.15820.93040.5511-0.27550.6109-0.3596-0.60960.51560.0218-0.14540.51340.03670.4002-28.01850.1173-16.589
132.40761.5619-1.51912-2.09973.083-0.0983-0.4473-0.7571.86470.911-0.70981.3424-1.232-0.81271.0764-0.2576-0.26240.70590.24910.852-36.3559-10.9612-19.9059
144.9698-0.8280.57961.20662.38385.82450.21250.3082-0.1775-0.33120.239-0.84030.07670.088-0.45151.25810.01540.00460.4715-0.07120.5448-20.8697-11.2328-31.2573
153.40710.9315-1.22935.5517-0.97017.0770.1799-0.3686-0.6160.12780.2326-0.04850.8652-0.0751-0.41260.82540.1057-0.22680.53230.10040.5566-25.1727-9.6049-8.7734
163.77390.6608-0.8676.6751-2.77998.14510.12050.2748-0.0436-0.35530.3243-2.27940.7439-0.0303-0.44481.2626-0.0133-0.0030.6655-0.09080.4545-22.28060.9134-28.7622
174.18640.61420.36243.12482.36753.1192-0.69741.82821.05870.56130.32220.43320.46631.21060.37521.7345-0.07180.00671.02620.21750.8118-15.4862-28.6932-9.1623
183.1445-1.0851-0.49137.5456-1.76138.58680.188-0.2044-0.0445-0.2349-0.0834-0.13641.23090.3711-0.10460.50570.01970.03110.32780.00750.3835-23.227423.3743-49.5491
194.3357-0.3972-2.86056.9834-1.14155.96520.25360.2972-0.3088-0.2347-0.159-1.41551.29360.086-0.09460.88780.10140.03560.4977-0.00330.5381-20.386923.7426-63.8716
208.4448-3.51977.48858.3845-5.89052-1.8141-1.72940.9413-0.97260.32241.4584-1.26920.12381.49171.12420.2374-0.27531.44040.03251.3061-1.974127.6698-45.8293
215.1499-1.8168-0.16668.3357-1.04396.46790.299-0.0320.113-0.1694-0.0532-0.64770.08060.5662-0.24580.307-0.06820.12330.41520.0170.3888-23.307433.0645-54.7235
223.19340.1928-3.13589.63890.78316.64610.6121.0784-0.55170.2128-0.4099-2.50240.9620.2511-0.20211.32580.1253-0.02710.6286-0.10550.458-23.823724.7374-68.7807
232.32352.26622.17314.4634-2.764120.54462.0383-0.1976-1.6044-1.4254-2.82211.15251.06430.88081.11250.34570.25751.26770.11930.8075-13.289732.7581-72.8189
245.685-1.62411.94793.6071-1.78156.50790.26310.37220.4033-0.432-0.261-0.2534-0.22591.3636-0.00210.53520.06740.31770.88670.04240.7236-12.423733.1443-58.3331
251.8945-1.56560.66238.4054-4.27137.23510.0788-0.06980.23050.51360.37140.6525-1.071-0.2514-0.45020.38520.07510.18060.422-0.00450.468-27.902341.6192-45.7944
262.242-0.0589-0.01024.86732.55291.3392-0.05650.25970.53591.26050.60540.9958-1.4363-1.138-0.54891.21980.38080.30330.70970.15540.7522-35.829252.813-42.2254
273.19061.3183-0.98190.91971.26947.78390.1265-0.42630.434-0.186-0.13931.0035-1.3920.16280.01281.382-0.1080.01580.6025-0.11140.6044-20.795353.0459-31.4484
284.316-0.47471.44662.4862-1.14398.55640.02980.46240.1763-0.0880.14750.5519-1.86270.4268-0.17730.9896-0.09150.13940.442-0.08240.696-23.121754.6014-45.5625
296.5313-2.44963.0562-3.992420.21850.64670.4325-0.1579-0.1987-0.6729-0.98420.3807-0.01980.5045-0.03080.17630.46720.04380.4516-25.613648.9178-59.0123
303.5302-1.50690.89242-2.98957.6424-0.1538-0.38650.1713-0.45040.1372.5258-1.03760.32880.01671.0895-0.049-0.00340.5753-0.09770.4568-22.236441.3242-33.816
319.77254.7327-3.81512-3.73439.556-0.1203-1.6583-2.3601-0.759-0.89821.621.05711.12781.01851.35410.0486-0.0420.7110.13430.7801-14.963970.9874-54.662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 92 )
6X-RAY DIFFRACTION6chain 'A' and (resid 93 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 114 )
8X-RAY DIFFRACTION8chain 'A' and (resid 115 through 133 )
9X-RAY DIFFRACTION9chain 'A' and (resid 134 through 157 )
10X-RAY DIFFRACTION10chain 'A' and (resid 158 through 168 )
11X-RAY DIFFRACTION11chain 'A' and (resid 169 through 190 )
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 69 )
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 89 )
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 114 )
15X-RAY DIFFRACTION15chain 'B' and (resid 115 through 161 )
16X-RAY DIFFRACTION16chain 'B' and (resid 162 through 196 )
17X-RAY DIFFRACTION17chain 'B' and (resid 197 through 207 )
18X-RAY DIFFRACTION18chain 'C' and (resid 6 through 52 )
19X-RAY DIFFRACTION19chain 'C' and (resid 53 through 104 )
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 113 )
21X-RAY DIFFRACTION21chain 'C' and (resid 114 through 147 )
22X-RAY DIFFRACTION22chain 'C' and (resid 148 through 157 )
23X-RAY DIFFRACTION23chain 'C' and (resid 158 through 168 )
24X-RAY DIFFRACTION24chain 'C' and (resid 169 through 190 )
25X-RAY DIFFRACTION25chain 'D' and (resid 3 through 69 )
26X-RAY DIFFRACTION26chain 'D' and (resid 70 through 89 )
27X-RAY DIFFRACTION27chain 'D' and (resid 90 through 114 )
28X-RAY DIFFRACTION28chain 'D' and (resid 115 through 133 )
29X-RAY DIFFRACTION29chain 'D' and (resid 134 through 161 )
30X-RAY DIFFRACTION30chain 'D' and (resid 162 through 196 )
31X-RAY DIFFRACTION31chain 'D' and (resid 197 through 207 )

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