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- PDB-4gsj: Crystal structure of Atg7 NTD K14A F16A D18A mutant -

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Basic information

Entry
Database: PDB / ID: 4gsj
TitleCrystal structure of Atg7 NTD K14A F16A D18A mutant
ComponentsUbiquitin-like modifier-activating enzyme ATG7
KeywordsPROTEIN TRANSPORT / Ubiquitin-like protein activation enzyme
Function / homology
Function and homology information


Atg12 activating enzyme activity / Atg8 activating enzyme activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus ...Atg12 activating enzyme activity / Atg8 activating enzyme activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phagophore assembly site / Neutrophil degranulation / macroautophagy / autophagy / protein transport / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like modifier-activating enzyme Atg7 / 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 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family
Similarity search - Domain/homology
CITRIC ACID / ISOPROPYL ALCOHOL / Ubiquitin-like modifier-activating enzyme ATG7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsKaiser, S.E. / Mao, K. / Taherbhoy, A.M. / Yu, S. / Olszewski, J.L. / Duda, D.M. / Kurinov, I. / Deng, A. / Fenn, T.D. / Klionsky, D.J. / Schulman, B.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures.
Authors: Kaiser, S.E. / Mao, K. / Taherbhoy, A.M. / Yu, S. / Olszewski, J.L. / Duda, D.M. / Kurinov, I. / Deng, A. / Fenn, T.D. / Klionsky, D.J. / Schulman, B.A.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ubiquitin-like modifier-activating enzyme ATG7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7978
Polymers33,2441
Non-polymers5537
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.826, 74.631, 76.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-307-

IPA

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme ATG7 / ATG12-activating enzyme E1 ATG7 / Autophagy-related protein 7 / Cytoplasm to vacuole targeting protein 2


Mass: 33244.078 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-289) / Mutation: K14A, F16A, D18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APG7, ATG7, CVT2, YHR171W / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: P38862
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 7.2% isopropanol, 50 mM citrate buffer, pH 4.1, 0.1 M potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.695→50 Å / Num. all: 36581 / Num. obs: 35213 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Χ2: 1.967 / Net I/σ(I): 46.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.695-1.7640.31627600.698177.4
1.76-1.834.80.25831930.871187.8
1.83-1.916.10.2134831.062197.1
1.91-2.027.20.16336161.3621100
2.02-2.147.20.12436231.6961100
2.14-2.317.10.09736152.041100
2.31-2.547.10.07936652.1881100
2.54-2.917.10.06636642.4971100
2.91-3.6670.05737153.161100
3.66-506.70.04338792.628199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T7F

3t7f


Resolution: 1.695→45.612 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8385 / SU ML: 0.4 / σ(F): 0 / Phase error: 22.7 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 1757 5 %RANDOM
Rwork0.176 ---
all0.1777 36828 --
obs0.1777 35168 95.5 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.801 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 93.03 Å2 / Biso mean: 30.5885 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1--8.1523 Å2-0 Å20 Å2
2--0.041 Å2-0 Å2
3---8.1113 Å2
Refinement stepCycle: LAST / Resolution: 1.695→45.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 37 257 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062418
X-RAY DIFFRACTIONf_angle_d1.0053278
X-RAY DIFFRACTIONf_chiral_restr0.069369
X-RAY DIFFRACTIONf_plane_restr0.004419
X-RAY DIFFRACTIONf_dihedral_angle_d13.313899
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.695-1.74080.3202770.26231806188368
1.7408-1.7920.26541270.21552213234084
1.792-1.84990.26651390.20322412255192
1.8499-1.9160.2681270.20272626275398
1.916-1.99270.26511320.178626562788100
1.9927-2.08340.21971390.176126712810100
2.0834-2.19330.21571250.171626842809100
2.1933-2.33070.21391390.172326822821100
2.3307-2.51060.22811360.178526702806100
2.5106-2.76320.22391420.191227042846100
2.7632-3.1630.19531470.181327082855100
3.163-3.98470.20181490.160527382887100
3.9847-45.62870.17281780.166528413019100
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)
11.44880.6126-0.65941.461-0.31081.321-0.21230.2511-0.1259-0.41050.1487-0.04550.3389-0.05610.07430.2043-0.00040.00350.1959-0.04490.168720.8618-16.8623-24.3678
22.28971.4440.19862.71360.12941.3196-0.00620.6596-0.3255-0.62190.16710.42680.3226-0.26750.07260.2818-0.0594-0.0950.30660.01920.285518.7038-12.1169-28.9972
34.26690.0645-0.09041.9536-0.07012.4647-0.00660.07590.0584-0.0404-0.0006-0.2285-0.0540.2922-0.02180.1563-0.0031-0.00040.14130.00950.123521.314-5.1245-16.2747
44.2172-0.5419-3.2672.3360.64945.6468-0.08650.0316-0.0511-0.27450.0261-0.37210.40840.46970.03120.14860.04110.03060.15940.0150.164630.3564-13.1963-23.1976
52.44220.1926-0.03511.6614-0.14681.4217-0.04150.054-0.1119-0.03840.0260.03110.0507-0.07630.00610.1413-0.00940.01130.11490.00240.14444.0489-16.6341-7.8156
62.64860.41940.06272.9212-0.43663.8285-0.2431-0.3156-0.18780.15990.0943-0.34050.3130.3450.03460.05750.0207-0.00050.03230.02160.137628.0552-14.7741-12.8702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:69)A-1 - 69
2X-RAY DIFFRACTION2(chain A and resid 70:90)A70 - 90
3X-RAY DIFFRACTION3(chain A and resid 91:124)A91 - 124
4X-RAY DIFFRACTION4(chain A and resid 125:147)A125 - 147
5X-RAY DIFFRACTION5(chain A and resid 148:258)A148 - 258
6X-RAY DIFFRACTION6(chain A and resid 259:289)A259 - 289

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