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- PDB-3vqi: Crystal structure of Kluyveromyces marxianus Atg5 -

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Basic information

Entry
Database: PDB / ID: 3vqi
TitleCrystal structure of Kluyveromyces marxianus Atg5
ComponentsAtg5
KeywordsPROTEIN TRANSPORT / autophagy / E3-like / Ubiquitin-fold / Atg16 / Atg12 / pre-autophagosomal structure / Protein turnover
Function / homology
Function and homology information


: / : / cargo receptor ligand activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / phagophore / vacuole-isolation membrane contact site / cytoplasm to vacuole targeting by the Cvt pathway / autophagy of mitochondrion ...: / : / cargo receptor ligand activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / phagophore / vacuole-isolation membrane contact site / cytoplasm to vacuole targeting by the Cvt pathway / autophagy of mitochondrion / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / autophagosome / enzyme activator activity / cytosol
Similarity search - Function
Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB domain / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll ...Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB domain / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 5
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYamaguchi, M. / Noda, N.N. / Yamamoto, H. / Shima, T. / Kumeta, H. / Kobashigawa, Y. / Akada, R. / Ohsumi, Y. / Inagaki, F.
CitationJournal: Structure / Year: 2012
Title: Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate
Authors: Yamaguchi, M. / Noda, N.N. / Yamamoto, H. / Shima, T. / Kumeta, H. / Kobashigawa, Y. / Akada, R. / Ohsumi, Y. / Inagaki, F.
History
DepositionMar 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atg5
B: Atg5
C: Atg5
D: Atg5
E: Atg5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,00223
Polymers157,8465
Non-polymers2,15618
Water1,38777
1
A: Atg5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0965
Polymers31,5691
Non-polymers5264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atg5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1926
Polymers31,5691
Non-polymers6235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Atg5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7613
Polymers31,5691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Atg5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7613
Polymers31,5691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Atg5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1926
Polymers31,5691
Non-polymers6235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.700, 81.900, 158.520
Angle α, β, γ (deg.)90.00, 92.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Atg5 /


Mass: 31569.182 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W0T4V8*PLUS
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT EXIST AT THE TIME OF PROCESSING.

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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: 3.4 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.6M (NH4)2SO4, 2% PEG 400, 0.1M HEPES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 84853 / Num. obs: 83071 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.44 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DYO

2dyo


Resolution: 2.5→35.15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 451753.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 7022 10.1 %RANDOM
Rwork0.238 ---
all0.241 73676 --
obs0.238 69845 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1476 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 62.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.27 Å20 Å2-3.87 Å2
2--11.78 Å20 Å2
3----3.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9844 0 120 77 10041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 1006 9.7 %
Rwork0.332 9335 -
obs-10341 84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6epe.paramepe.top

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