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- PDB-3vx7: Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex -

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Basic information

Entry
Database: PDB / ID: 3vx7
TitleCrystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex
Components
  • E1
  • E2
KeywordsLIGASE / ubiquitin conjugation / E1-E2 complex
Function / homology
Function and homology information


ubiquitin-like protein transferase activity / phagophore assembly site membrane / Transferases; Acyltransferases; Aminoacyltransferases / autophagy / protein transport
Similarity search - Function
Yope Regulator; Chain: A, - #50 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E1 / Ubiquitin-like-conjugating enzyme ATG10
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. ...Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / Inagaki, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.
Authors: Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / Inagaki, F.
History
DepositionSep 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E1
B: E2


Theoretical massNumber of molelcules
Total (without water)49,9522
Polymers49,9522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-5 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.935, 185.935, 185.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein E1


Mass: 32213.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Plasmid: pGBHPS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: L7MTK3*PLUS
#2: Protein E2


Mass: 17738.104 Da / Num. of mol.: 1
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: W0TH64*PLUS
Sequence detailsSEQUENCE DATABASE REFERENCE FOR EACH CHAIN DOES NOT CURRENTLY EXIST.

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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: 5.36 Å3/Da / Density % sol: 77.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.8M sodium phosphate, 0.7M potassium phosphate, 0.2M lithium sulfate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.69 Å / Num. all: 18726 / Num. obs: 18382 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rsym value: 0.068 / Net I/σ(I): 24.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 9.1 / Rsym value: 0.386 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VX6

3vx6


Resolution: 3.2→49.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 215793.01 / 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
Rfree0.288 1641 10 %RANDOM
Rwork0.249 ---
all0.253 18710 --
obs0.249 16465 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.718 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 91.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 0 0 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 251 10.1 %
Rwork0.331 2245 -
obs-2496 82.4 %
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

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