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- PDB-7aa7: Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1 -

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Basic information

Entry
Database: PDB / ID: 7aa7
TitleStructure of SCOC pS12/pS18 LIR motif bound to GABARAPL1
Components
  • Gamma-aminobutyric acid receptor-associated protein-like 1
  • pS12/pS18 SCOC LIR
KeywordsSIGNALING PROTEIN / SCOC / ATG8 / LIR
Function / homology
Function and homology information


glycophagy / Tat protein binding / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation ...glycophagy / Tat protein binding / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / cytoplasmic vesicle membrane / phospholipid binding / microtubule / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
sulfoacetic acid / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLee, R. / Mouilleron, S. / Wirth, M. / Zhang, W. / O Reilly, N. / Dhira, J. / Tooze, S.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity.
Authors: Wirth, M. / Mouilleron, S. / Zhang, W. / Sjottem, E. / Princely Abudu, Y. / Jain, A. / Lauritz Olsvik, H. / Bruun, J.A. / Razi, M. / Jefferies, H.B.J. / Lee, R. / Joshi, D. / O'Reilly, N. / ...Authors: Wirth, M. / Mouilleron, S. / Zhang, W. / Sjottem, E. / Princely Abudu, Y. / Jain, A. / Lauritz Olsvik, H. / Bruun, J.A. / Razi, M. / Jefferies, H.B.J. / Lee, R. / Joshi, D. / O'Reilly, N. / Johansen, T. / Tooze, S.A.
History
DepositionSep 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Gamma-aminobutyric acid receptor-associated protein-like 1
P: pS12/pS18 SCOC LIR
Q: pS12/pS18 SCOC LIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3086
Polymers32,0284
Non-polymers2802
Water3,009167
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
P: pS12/pS18 SCOC LIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1543
Polymers16,0142
Non-polymers1401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-13 kcal/mol
Surface area6930 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
Q: pS12/pS18 SCOC LIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1543
Polymers16,0142
Non-polymers1401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-15 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.364, 37.169, 62.482
Angle α, β, γ (deg.)81.751, 89.602, 67.818
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14598.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8
#2: Protein/peptide pS12/pS18 SCOC LIR


Mass: 1415.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SAT / sulfoacetic acid


Mass: 140.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M MES pH 6.5, 3.5M AMSO4, 1% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→31.92 Å / Num. obs: 41242 / % possible obs: 99.5 % / Redundancy: 3 % / Biso Wilson estimate: 11.98 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 2051 / CC1/2: 0.46 / Rpim(I) all: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HOI

6hoi


Resolution: 1.45→31.92 Å / SU ML: 0.1573 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.8909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1894 1970 4.79 %
Rwork0.1509 39189 -
obs0.1528 41159 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.89 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 16 167 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982191
X-RAY DIFFRACTIONf_angle_d1.12343002
X-RAY DIFFRACTIONf_chiral_restr0.0955319
X-RAY DIFFRACTIONf_plane_restr0.0075386
X-RAY DIFFRACTIONf_dihedral_angle_d22.1162837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.29121500.21422852X-RAY DIFFRACTION98.23
1.49-1.530.29491510.20022696X-RAY DIFFRACTION98.65
1.53-1.570.24161430.17682793X-RAY DIFFRACTION98.72
1.57-1.620.21121440.15992785X-RAY DIFFRACTION99.52
1.62-1.680.20461390.14692821X-RAY DIFFRACTION99.23
1.68-1.750.20751150.13932783X-RAY DIFFRACTION99.14
1.75-1.830.17261330.1342808X-RAY DIFFRACTION99.46
1.83-1.920.2211350.13272799X-RAY DIFFRACTION99.22
1.92-2.040.1691220.12782829X-RAY DIFFRACTION99.53
2.04-2.20.16261520.13422834X-RAY DIFFRACTION99.77
2.2-2.420.2091170.14112791X-RAY DIFFRACTION99.66
2.42-2.770.191600.15462787X-RAY DIFFRACTION99.8
2.77-3.490.17211490.15862816X-RAY DIFFRACTION99.76
3.49-31.920.16831600.15372795X-RAY DIFFRACTION99.7

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