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- PDB-5azf: Crystal structure of LGG-1 complexed with a WEEL peptide -

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Basic information

Entry
Database: PDB / ID: 5azf
TitleCrystal structure of LGG-1 complexed with a WEEL peptide
Components
  • Protein lgg-1
  • peptide from Autophagy-related protein 19
KeywordsPROTEIN BINDING / Autophagy / Ubiquitin-like
Function / homology
Function and homology information


dauer larval development / Macroautophagy / Cvt complex / cellular response to toxic substance / vesicle organization / positive regulation of autophagosome assembly / xenophagy / phagophore assembly site membrane / GABA receptor binding / programmed cell death ...dauer larval development / Macroautophagy / Cvt complex / cellular response to toxic substance / vesicle organization / positive regulation of autophagosome assembly / xenophagy / phagophore assembly site membrane / GABA receptor binding / programmed cell death / plasma membrane repair / cellular response to nitrogen starvation / protein-containing complex localization / phagophore assembly site / autophagy of mitochondrion / autophagosome membrane / necroptotic process / autophagosome assembly / autophagosome / : / lysosomal lumen / determination of adult lifespan / macroautophagy / autophagy / phagocytic vesicle membrane / protein transport / protein-macromolecule adaptor activity / response to heat / perikaryon / mitochondrial outer membrane / neuron projection / defense response to Gram-positive bacterium / neuronal cell body / dendrite / ubiquitin protein ligase binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg19/Atg34, C-terminal / Autophagy protein Atg19, Atg8-binding / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Autophagy-related protein 19 / Protein lgg-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWatanabe, Y. / Noda, N.N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan25111004 Japan
Ministry of Education, Culture, Sports, Science and Technology of Japan26870828 Japan
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy.
Authors: Wu, F. / Watanabe, Y. / Guo, X.Y. / Qi, X. / Wang, P. / Zhao, H.Y. / Wang, Z. / Fujioka, Y. / Zhang, H. / Ren, J.Q. / Fang, T.C. / Shen, Y.X. / Feng, W. / Hu, J.J. / Noda, N.N. / Zhang, H.
History
DepositionOct 5, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed ..._citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein lgg-1
B: Protein lgg-1
C: peptide from Autophagy-related protein 19
D: peptide from Autophagy-related protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,26718
Polymers29,7104
Non-polymers1,55714
Water7,404411
1
A: Protein lgg-1
C: peptide from Autophagy-related protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4177
Polymers14,8552
Non-polymers5625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-31 kcal/mol
Surface area7140 Å2
MethodPISA
2
B: Protein lgg-1
D: peptide from Autophagy-related protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,85011
Polymers14,8552
Non-polymers9959
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-59 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.280, 112.146, 35.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein lgg-1


Mass: 14279.358 Da / Num. of mol.: 2 / Fragment: UNP residues 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lgg-1, C32D5.9 / Plasmid: pGEX-6P / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q09490
#2: Protein/peptide peptide from Autophagy-related protein 19 / / Atg19 AIM


Mass: 575.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35193
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.5 M Sodium acetate, 50 mM HEPES, 25 mM Cadmium sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→29.4 Å / Num. obs: 51705 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EO6
Resolution: 1.6→29.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 98719.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5071 10.1 %RANDOM
Rwork0.201 ---
obs0.201 50395 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2602 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å20 Å20 Å2
2---0.36 Å20 Å2
3----3.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: 1 / Resolution: 1.6→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 18 411 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
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_it2.022
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 778 9.9 %
Rwork0.261 7067 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top

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