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- PDB-6yop: Structure of SAMM50 LIR bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6yop
TitleStructure of SAMM50 LIR bound to GABARAP
ComponentsSorting and assembly machinery component 50 homolog,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / LIR / SAMM50 / ATG8
Function / homology
Function and homology information


MIB complex / SAM complex / Cristae formation / inner mitochondrial membrane organization / mitochondrial respiratory chain complex assembly / positive regulation of protein K48-linked ubiquitination / protein insertion into mitochondrial outer membrane / cristae formation / regulation of Rac protein signal transduction / GABA receptor binding ...MIB complex / SAM complex / Cristae formation / inner mitochondrial membrane organization / mitochondrial respiratory chain complex assembly / positive regulation of protein K48-linked ubiquitination / protein insertion into mitochondrial outer membrane / cristae formation / regulation of Rac protein signal transduction / GABA receptor binding / Mitochondrial protein import / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / protein import into mitochondrial matrix / smooth endoplasmic reticulum / autophagosome membrane / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / autophagosome maturation / RAC2 GTPase cycle / beta-tubulin binding / protein targeting / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / mitochondrial outer membrane / lysosome / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Sorting and assembly machinery component 50 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMouilleron, S. / Wenxin, Z. / Johansen, T. / Tooze, S. / Abudu, Y.P. / Lamark, T.
CitationJournal: To Be Published
Title: Structure of SAMM50 LIR bound to GABARAP
Authors: Mouilleron, S. / Wenxin, Z. / Johansen, T. / Tooze, S. / Abudu, Y.P. / Lamark, T.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting and assembly machinery component 50 homolog,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)15,9451
Polymers15,9451
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.323, 101.323, 101.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

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Components

#1: Protein Sorting and assembly machinery component 50 homolog,Gamma-aminobutyric acid receptor-associated protein / Transformation-related gene 3 protein / TRG-3 / GABA(A) receptor-associated protein / MM46


Mass: 15945.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMM50, SAM50, CGI-51, TRG3, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y512, UniProt: O95166
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% v/v isopropanol, 0.1 M Na Acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→50.66 Å / Num. obs: 5665274 / % possible obs: 99.9 % / Redundancy: 81.1 % / Biso Wilson estimate: 15.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.01 / Net I/σ(I): 27.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 81.8 % / Rmerge(I) obs: 2.64 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 567531 / CC1/2: 0.76 / Rpim(I) all: 0.29 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.1→50.66 Å / SU ML: 0.1054 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.3818
RfactorNum. reflection% reflection
Rfree0.1588 3458 4.95 %
Rwork0.1381 --
obs0.1392 69849 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.96 Å2
Refinement stepCycle: LAST / Resolution: 1.1→50.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 0 177 1272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02271258
X-RAY DIFFRACTIONf_angle_d1.68311725
X-RAY DIFFRACTIONf_chiral_restr0.4302181
X-RAY DIFFRACTIONf_plane_restr0.0134230
X-RAY DIFFRACTIONf_dihedral_angle_d29.2445514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.271440.25692640X-RAY DIFFRACTION100
1.12-1.130.24421210.24072625X-RAY DIFFRACTION100
1.13-1.150.2421230.21712649X-RAY DIFFRACTION100
1.15-1.170.2331580.20542650X-RAY DIFFRACTION99.96
1.17-1.180.21071500.19362600X-RAY DIFFRACTION100
1.19-1.210.21551250.18172667X-RAY DIFFRACTION99.96
1.21-1.230.20631820.17092588X-RAY DIFFRACTION100
1.23-1.250.20521440.16752644X-RAY DIFFRACTION100
1.25-1.280.16421180.16342648X-RAY DIFFRACTION100
1.28-1.30.17381360.15082646X-RAY DIFFRACTION100
1.3-1.330.18841240.14472665X-RAY DIFFRACTION100
1.33-1.370.14861520.13712592X-RAY DIFFRACTION99.96
1.37-1.40.17611290.13292692X-RAY DIFFRACTION100
1.41-1.450.15761070.11942685X-RAY DIFFRACTION100
1.45-1.490.15261150.11872679X-RAY DIFFRACTION100
1.49-1.550.14561560.11182611X-RAY DIFFRACTION100
1.55-1.610.14021420.11012661X-RAY DIFFRACTION100
1.61-1.680.1431460.10942631X-RAY DIFFRACTION100
1.68-1.770.14771660.11222645X-RAY DIFFRACTION100
1.77-1.880.13741360.10952660X-RAY DIFFRACTION100
1.88-2.030.12351460.10462678X-RAY DIFFRACTION100
2.03-2.230.12181400.10632666X-RAY DIFFRACTION100
2.23-2.550.13691350.12272678X-RAY DIFFRACTION100
2.55-3.210.16351410.14952706X-RAY DIFFRACTION100
3.22-50.660.18261220.1622785X-RAY DIFFRACTION98.91

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