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- PDB-4ebr: Crystal structure of Autophagic E2, Atg10 -

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Basic information

Entry
Database: PDB / ID: 4ebr
TitleCrystal structure of Autophagic E2, Atg10
ComponentsUbiquitin-like-conjugating enzyme ATG10
KeywordsLIGASE / E2-Conjugating enzyme / Autophagy / protein binding / Atg3 / Atg5 / Atg7 / Atg12 / Thiolation
Function / homology
Function and homology information


Atg12 transferase activity / : / protein modification by small protein conjugation / cytoplasm to vacuole targeting by the Cvt pathway / autophagy of mitochondrion / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / Transferases; Acyltransferases; Aminoacyltransferases / macroautophagy
Similarity search - Function
Ubiquitin-like-conjugating enzyme Atg10 / Yope Regulator; Chain: A, - #50 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ubiquitin-like-conjugating enzyme ATG10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.701 Å
AuthorsHong, S.B. / Kim, B.W. / Kim, J.H. / Song, H.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the autophagic E2 enzyme Atg10
Authors: Hong, S.B. / Kim, B.W. / Kim, J.H. / Song, H.K.
History
DepositionMar 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like-conjugating enzyme ATG10
B: Ubiquitin-like-conjugating enzyme ATG10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6204
Polymers40,2192
Non-polymers4012
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-62 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.833, 127.833, 169.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21B-304-

HOH

31B-315-

HOH

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Components

#1: Protein Ubiquitin-like-conjugating enzyme ATG10 / Autophagy-related protein 10


Mass: 20109.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508, S288c / Gene: ATG10, APG10, YLL042C / Production host: Escherichia coli (E. coli)
References: UniProt: Q07879, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.97 Å3/Da / Density % sol: 75.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM bis-Tris-HCl (pH 6.15), 3M NaCl, 1mM 1,4-diacetoxymercury-2,3-dimetoxybutane, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.97951, 0.97966, 0.96
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 7, 2009
ADSC QUANTUM 2102CCDFeb 8, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorMADMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979511
20.979661
30.961
411
ReflectionResolution: 2.701→27.835 Å / Num. all: 23338 / Num. obs: 23007 / % possible obs: 98.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.7→2.75 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.701→27.835 Å / SU ML: 0.36 / σ(F): 0.15 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 1886 8.67 %random
Rwork0.2107 ---
obs0.224 21751 94.34 %-
all-23056 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.819 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7844 Å20 Å2-0 Å2
2--0.7844 Å20 Å2
3----1.5688 Å2
Refinement stepCycle: LAST / Resolution: 2.701→27.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 2 36 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012674
X-RAY DIFFRACTIONf_angle_d1.4183636
X-RAY DIFFRACTIONf_dihedral_angle_d16.726964
X-RAY DIFFRACTIONf_chiral_restr0.099402
X-RAY DIFFRACTIONf_plane_restr0.007450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7012-2.77420.36011210.316129582
2.7742-2.85580.32751240.3086136086
2.8558-2.94780.33351440.2662153896
2.9478-3.05310.27961440.253155098
3.0531-3.17520.30191460.2412152796
3.1752-3.31940.24961470.2319150494
3.3194-3.49410.24811410.2129146793
3.4941-3.71260.26291440.2097154495
3.7126-3.99850.20461520.1779154596
3.9985-4.39940.19391500.1653156997
4.3994-5.03280.17431520.1482161598
5.0328-6.32850.21171570.2088164399
6.3285-27.83670.24991640.2386170896
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)
18.2972-3.81390.486.21772.07026.42290.0233-0.0441.1589-0.61320.5121-0.8412-1.12390.6925-0.52420.7524-0.13290.08550.4343-0.13790.47466.748460.9172113.8053
23.9434-3.757-3.40383.79533.60625.13650.0363-0.0538-0.0463-0.11160.2254-0.09190.11230.7918-0.25750.50720.0344-0.01550.5105-0.05680.355669.176245.0089108.3175
31.6746-0.9461-0.9330.59840.46930.53230.0703-1.7062-0.41720.5579-0.4314-1.3010.492-0.14870.25371.21570.0436-0.03321.03040.25431.040261.554438.783119.4785
44.194-0.08971.90457.7535.67168.9192-0.0218-0.51560.11590.47650.31770.0563-0.2252-0.3791-0.28640.41290.1028-0.00390.47040.06330.316961.71252.9009118.7661
53.9089-2.90681.07483.1390.79344.743-0.2503-1.21760.37591.09220.06860.92750.479-0.1020.42260.48140.18130.08760.5446-0.01810.452137.039542.6006121.6993
65.3534-0.0882-1.07836.7761.29743.9116-0.09060.4659-0.6392-0.0844-0.4680.99810.6096-0.45340.44010.33160.10230.07530.3602-0.12840.608536.89435.6351108.5384
71.4547-2.4525-1.43675.23814.81076.87560.36190.3039-0.2359-0.52980.0375-0.0207-0.29940.1642-0.48020.46380.13970.02170.49-0.06950.637145.195134.918995.7244
80.2013-0.0921-0.43450.10340.4772.33040.33211.68060.4826-1.3565-1.2013-0.35150.4556-0.83081.43871.02060.1968-0.04650.9618-0.21791.120244.97149.917498.7665
97.042-3.3638-2.42042.71923.55836.4189-0.14810.03530.34370.49880.264-0.55410.10810.4563-0.2380.3867-0.0070.0280.4949-0.04510.434247.212442.6096107.7213
108.1702-3.6846-2.796.84071.41538.6991-0.5371-0.12540.43380.0382-0.13080.3783-0.89190.28050.32530.30.07630.040.3003-0.04960.516833.363649.8118113.2625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ -1:31)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 32:106)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 107:118)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 119:165)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ -1:17)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 18:74)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 75:105)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 106:118)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 119:137)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 138:165)

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