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- PDB-4gsl: Crystal structure of an Atg7-Atg3 crosslinked complex -

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Basic information

Entry
Database: PDB / ID: 4gsl
TitleCrystal structure of an Atg7-Atg3 crosslinked complex
Components
  • Autophagy-related protein 3
  • Ubiquitin-like modifier-activating enzyme ATG7
KeywordsPROTEIN TRANSPORT / Ubiquitin-like protein activation enzyme / Ubiquitin-like protein transfer enzyme
Function / homology
Function and homology information


Atg8-family conjugating enzyme activity / Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / phagophore / Macroautophagy / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway ...Atg8-family conjugating enzyme activity / Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / phagophore / Macroautophagy / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / piecemeal microautophagy of the nucleus / phagophore assembly site / protein targeting to membrane / cellular response to nitrogen starvation / autophagy of mitochondrion / Antigen processing: Ubiquitination & Proteasome degradation / autophagosome assembly / Neutrophil degranulation / macroautophagy / autophagy / mitochondrion / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 / THIF-type NAD/FAD binding fold ...: / 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 / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme ATG7 / Autophagy-related protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 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 1.3Sep 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
C: Autophagy-related protein 3
D: Autophagy-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,4656
Polymers211,3344
Non-polymers1312
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-96 kcal/mol
Surface area63660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)281.556, 125.083, 71.079
Angle α, β, γ (deg.)90.000, 103.320, 90.000
Int Tables number5
Space group name H-MC121

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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: 69692.211 Da / Num. of mol.: 2 / Fragment: UNP residues 1-613
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 Autophagy-related protein 3 / Autophagy-related E2-like conjugation enzyme ATG3


Mass: 35974.973 Da / Num. of mol.: 2 / Mutation: C41A, C76A, C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APG3, ATG3, AUT1, N2040, YNR007C / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P40344
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM sodium citrate, pH 5.8, 13.5% PEG4000, 10% isopropanol, 5% dioxane, 88 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 65155 / Num. obs: 64845 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.079 / Χ2: 3.615 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.840.55664000.609199
2.8-2.914.10.38464440.648199.1
2.91-3.044.10.2864490.685199.4
3.04-3.24.10.264640.748199.3
3.2-3.44.10.12964451199.6
3.4-3.664.10.08964591.669199.7
3.66-4.034.10.06765051.976199.6
4.03-4.624.10.05365113.378199.8
4.62-5.8140.05965254.587199.9
5.81-403.90.05664321.07199.9

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Processing

Software
NameVersionClassificationNB
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 ENTRIES 3T7E, 3T7F, AND 2DYT

3t7e

3t7f

2dyt


Resolution: 2.703→37.073 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.82 / σ(F): 0 / σ(I): 0 / Phase error: 24.14 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1901 2.94 %RANDOM
Rwork0.1927 ---
all0.1943 64763 --
obs0.1943 64763 98.66 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.889 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 224.79 Å2 / Biso mean: 70.5395 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-6.8972 Å2-0 Å2-4.4035 Å2
2---6.0097 Å20 Å2
3----0.8876 Å2
Refinement stepCycle: LAST / Resolution: 2.703→37.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12498 0 2 43 12543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912782
X-RAY DIFFRACTIONf_angle_d1.21417321
X-RAY DIFFRACTIONf_chiral_restr0.0811970
X-RAY DIFFRACTIONf_plane_restr0.0062197
X-RAY DIFFRACTIONf_dihedral_angle_d17.1714756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.703-2.77020.36711230.29164022414588
2.7702-2.8450.36041250.27374483460899
2.845-2.92870.33011490.24564477462699
2.9287-3.02320.29661390.22494486462599
3.0232-3.13120.30681420.21774524466699
3.1312-3.25650.25091410.203645004641100
3.2565-3.40460.30721300.21944500463099
3.4046-3.5840.23631360.198145604696100
3.584-3.80830.20681380.176244904628100
3.8083-4.1020.23131370.176145394676100
4.102-4.51420.20851330.165745624695100
4.5142-5.16590.2311360.156345564692100
5.1659-6.50280.24181340.209845914725100
6.5028-37.07680.21981380.18124572471098
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)
10.9342-0.531-0.01481.0321-0.01540.3273-0.0660.06740.293-0.1311-0.01770.14640.1012-0.07410.05570.2037-0.0504-0.05750.2424-0.06910.171647.2135-67.3743-31.223
20.81950.40860.41871.05550.46660.63080.2378-0.0186-0.33370.0416-0.0140.14330.0836-0.0935-0.04790.12020.0601-0.02580.1273-0.02880.085341.0713-27.812-0.7874
32.94550.04790.22191.9698-0.03113.6370.02380.7559-0.1415-0.9625-0.01210.71530.0813-0.6597-0.07150.591-0.0014-0.24820.3677-0.06210.494139.1109-9.9066-14.2146
42.86320.2066-0.22292.2564-0.19043.0585-0.0966-0.37230.04040.3893-0.01861.19980.1038-1.1010.01680.3794-0.00630.10370.4857-0.11020.797339.0288-86.9611-19.889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(Chain A)A0
2X-RAY DIFFRACTION2(Chain B)B0
3X-RAY DIFFRACTION3(Chain C)C0
4X-RAY DIFFRACTION4(Chain D)D0

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