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- PDB-4gsk: Crystal structure of an Atg7-Atg10 crosslinked complex -

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Basic information

Entry
Database: PDB / ID: 4gsk
TitleCrystal structure of an Atg7-Atg10 crosslinked complex
Components
  • Ubiquitin-like modifier-activating enzyme ATG7
  • Ubiquitin-like-conjugating enzyme ATG10
KeywordsPROTEIN TRANSPORT/LIGASE / Ubiquitin-like protein activation enzyme / Ubiquitin-like protein transfer enzyme / PROTEIN TRANSPORT-LIGASE complex
Function / homology
Function and homology information


Atg12 transferase activity / Atg12 activating enzyme activity / Atg8 activating enzyme activity / : / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion ...Atg12 transferase activity / Atg12 activating enzyme activity / Atg8 activating enzyme activity / : / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to nitrogen starvation / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / macroautophagy / autophagy / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-like-conjugating enzyme Atg10 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / 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 ...Ubiquitin-like-conjugating enzyme Atg10 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / 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 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme ATG7 / Ubiquitin-like-conjugating enzyme ATG10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
B: Ubiquitin-like modifier-activating enzyme ATG7
Y: Ubiquitin-like-conjugating enzyme ATG10
Z: Ubiquitin-like-conjugating enzyme ATG10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6826
Polymers179,5524
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13090 Å2
ΔGint-73 kcal/mol
Surface area58380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.556, 146.186, 108.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: 69628.016 Da / Num. of mol.: 2 / Fragment: UNP residues 1-613 / Mutation: C39S, C195S, C375A
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: Protein Ubiquitin-like-conjugating enzyme ATG10 / Autophagy-related protein 10


Mass: 20147.807 Da / Num. of mol.: 2 / Mutation: C26S, C137S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APG10, ATG10, YLL042C / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q07879, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 76.5 mM sodium/potassium phosphate, pH 6.5, 9 mM Tris, pH 8.5, 153 mM sodium chloride, 100 mM glycine, 72 mM sodium/potassium tartrate, 19.125% PEG1000, 0.045% PEG5000 MME, 4.5% dioxane, ...Details: 76.5 mM sodium/potassium phosphate, pH 6.5, 9 mM Tris, pH 8.5, 153 mM sodium chloride, 100 mM glycine, 72 mM sodium/potassium tartrate, 19.125% PEG1000, 0.045% PEG5000 MME, 4.5% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 43151 / Num. obs: 42754 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.134 / Χ2: 1.083 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.30.76542260.838199.3
3-3.123.30.58442230.833199.3
3.12-3.273.20.42442290.88198.9
3.27-3.4430.29841800.941198.5
3.44-3.653.20.20642271.052199
3.65-3.943.30.14742551.137199.3
3.94-4.333.20.09942701.253199.1
4.33-4.963.10.07542771.253198.8
4.96-6.243.20.07743461.142199.6
6.24-5030.07245211.523198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1000refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3T7E AND 3T7F

3t7e

3t7f


Resolution: 2.9→49.565 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 0 / Phase error: 29.52 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 2154 5.04 %RANDOM
Rwork0.2362 ---
all0.2387 43201 --
obs0.2387 42709 98.9 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.665 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 105.49 Å2 / Biso mean: 79.6706 Å2 / Biso min: 57.16 Å2
Baniso -1Baniso -2Baniso -3
1--27.8803 Å2-0 Å2-0 Å2
2---2.9421 Å2-0 Å2
3----30.4193 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11406 0 2 0 11408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411680
X-RAY DIFFRACTIONf_angle_d0.84215832
X-RAY DIFFRACTIONf_chiral_restr0.0631796
X-RAY DIFFRACTIONf_plane_restr0.0041994
X-RAY DIFFRACTIONf_dihedral_angle_d13.8744323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.96760.35651370.30992594273196
2.9676-3.04180.35631400.318926972837100
3.0418-3.1240.37831490.30472658280799
3.124-3.2160.34661400.29362665280599
3.216-3.31970.30851450.28022673281899
3.3197-3.43840.31481430.26432661280498
3.4384-3.5760.30841530.25172674282799
3.576-3.73870.31361490.22962678282799
3.7387-3.93570.27961460.23112675282199
3.9357-4.18220.24091280.21312744287299
4.1822-4.50490.24421520.19972691284398
4.5049-4.95790.2431170.19372738285599
4.9579-5.67440.25361490.219627442893100
5.6744-7.14570.34611450.27232767291299
7.1457-49.57220.24811610.20762896305799

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