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- PDB-7eu4: Crystal structure of plant ATG12 complexed with the AIM12 of ATG3 -

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Basic information

Entry
Database: PDB / ID: 7eu4
TitleCrystal structure of plant ATG12 complexed with the AIM12 of ATG3
Components
  • AIM12 from Autophagy-related protein 3
  • Ubiquitin-like protein ATG12B
KeywordsPLANT PROTEIN / autophagy / ubiquitin-like modifier / E2
Function / homology
Function and homology information


Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / nucleophagy / phagophore assembly site membrane / autophagosome assembly / autophagy / protein transport / cytoplasm
Similarity search - Function
Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / : / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 3 / Ubiquitin-like protein ATG12B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMatoba, K. / Noda, N.N.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25111004 Japan
Japan Society for the Promotion of Science (JSPS)18H03989 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Society for the Promotion of Science (JSPS)25871076 Japan
Japan Society for the Promotion of Science (JSPS)15K21608 Japan
Japan Society for the Promotion of Science (JSPS)18K06097 Japan
Japan Science and TechnologyJPMJCR13M7 Japan
Japan Science and TechnologyJPMJCR20E3 Japan
CitationJournal: Biol.Pharm.Bull. / Year: 2021
Title: Atg12-Interacting Motif Is Crucial for E2-E3 Interaction in Plant Atg8 System.
Authors: Matoba, K. / Noda, N.N.
History
DepositionMay 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 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: Ubiquitin-like protein ATG12B
B: Ubiquitin-like protein ATG12B
C: Ubiquitin-like protein ATG12B
D: Ubiquitin-like protein ATG12B
E: Ubiquitin-like protein ATG12B
F: Ubiquitin-like protein ATG12B
G: Ubiquitin-like protein ATG12B
H: Ubiquitin-like protein ATG12B
I: Ubiquitin-like protein ATG12B
J: Ubiquitin-like protein ATG12B
K: Ubiquitin-like protein ATG12B
L: Ubiquitin-like protein ATG12B
M: Ubiquitin-like protein ATG12B
N: Ubiquitin-like protein ATG12B
O: AIM12 from Autophagy-related protein 3
P: AIM12 from Autophagy-related protein 3
Q: AIM12 from Autophagy-related protein 3
R: AIM12 from Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)152,73818
Polymers152,73818
Non-polymers00
Water00
1
A: Ubiquitin-like protein ATG12B
B: Ubiquitin-like protein ATG12B
O: AIM12 from Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)22,4003
Polymers22,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-like protein ATG12B
D: Ubiquitin-like protein ATG12B
P: AIM12 from Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)22,4003
Polymers22,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ubiquitin-like protein ATG12B
F: Ubiquitin-like protein ATG12B
Q: AIM12 from Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)22,4003
Polymers22,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ubiquitin-like protein ATG12B
H: Ubiquitin-like protein ATG12B
R: AIM12 from Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)22,4003
Polymers22,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Ubiquitin-like protein ATG12B
J: Ubiquitin-like protein ATG12B


Theoretical massNumber of molelcules
Total (without water)21,0462
Polymers21,0462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Ubiquitin-like protein ATG12B
L: Ubiquitin-like protein ATG12B


Theoretical massNumber of molelcules
Total (without water)21,0462
Polymers21,0462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Ubiquitin-like protein ATG12B
N: Ubiquitin-like protein ATG12B


Theoretical massNumber of molelcules
Total (without water)21,0462
Polymers21,0462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.471, 128.471, 163.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein
Ubiquitin-like protein ATG12B / Autophagy-related protein 12b / APG12-like protein b / AtAPG12b


Mass: 10522.900 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATG12B, APG12, APG12B, At3g13970, MDC16.9 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9LVK3
#2: Protein/peptide
AIM12 from Autophagy-related protein 3 / Autophagy-related E2-like conjugation enzyme ATG3 / AtAPG3 / Protein autophagy 3


Mass: 1354.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q0WWQ1

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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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 6~8% (w/v) PEG 3350, 100mM citrate buffer / PH range: 3.5-4.1

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→45.96 Å / Num. obs: 25048 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rsym value: 0.144 / Net I/σ(I): 7.1
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1227 / CC1/2: 0.452 / Rsym value: 0.767

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZ3

1wz3


Resolution: 3.2→45.96 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 --
Rwork0.238 --
obs-23805 94.99 %
Displacement parametersBiso mean: 80.71 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9301 0 0 0 9301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01149507
X-RAY DIFFRACTIONf_angle_d1.591712856
X-RAY DIFFRACTIONf_chiral_restr0.09251418
X-RAY DIFFRACTIONf_plane_restr0.01141670
X-RAY DIFFRACTIONf_dihedral_angle_d22.75033371

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