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- PDB-1eo6: CRYSTAL STRUCTURE OF GATE-16 -

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Basic information

Entry
Database: PDB / ID: 1eo6
TitleCRYSTAL STRUCTURE OF GATE-16
ComponentsGOLGI-ASSOCIATED ATPASE ENHANCER OF 16 KD
KeywordsPROTEIN BINDING / ubiquitin fold
Function / homology
Function and homology information


TBC/RABGAPs / Macroautophagy / protein localization to endoplasmic reticulum / intra-Golgi vesicle-mediated transport / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation ...TBC/RABGAPs / Macroautophagy / protein localization to endoplasmic reticulum / intra-Golgi vesicle-mediated transport / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / autophagosome / SNARE binding / protein transport / ATPase binding / cytoplasmic vesicle / Golgi membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / cytosol
Similarity search - Function
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
Gamma-aminobutyric acid receptor-associated protein-like 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPaz, Y. / Elazar, Z. / Fass, D.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Structure of GATE-16, membrane transport modulator and mammalian ortholog of autophagocytosis factor Aut7p.
Authors: Paz, Y. / Elazar, Z. / Fass, D.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Isolation and Characterization of a Novel Low Molecular Weight Protein Involved in Intra-Golgi Traffic
Authors: Legesse-Miller, A. / Sagiv, Y. / Porat, A. / Elazar, Z.
#2: Journal: Embo J. / Year: 2000
Title: GATE-16, a Membrane Transport Modulator Interacts with NSF and the Golgi v-SNARE GOS-28
Authors: Sagiv, Y. / Legesse-Miller, A. / Porat, A. / Elazar, Z.
History
DepositionMar 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: GOLGI-ASSOCIATED ATPASE ENHANCER OF 16 KD
B: GOLGI-ASSOCIATED ATPASE ENHANCER OF 16 KD


Theoretical massNumber of molelcules
Total (without water)27,3742
Polymers27,3742
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-8 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.30, 76.33, 49.71
Angle α, β, γ (deg.)90, 92.81, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GOLGI-ASSOCIATED ATPASE ENHANCER OF 16 KD / GATE-16


Mass: 13686.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: BRAIN / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: P60519
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, Tris, Calcium acetate, dimethyl sulfoxide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris1reservoir
2100 mMcalcium acetate1reservoir
322 %PEG80001reservoir
410 %1reservoirMe2SO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 27943 / Num. obs: 27335 / % possible obs: 97.8 % / Observed criterion σ(I): -1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.252 / Num. unique all: 2777 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 1.8 Å
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1895 -random
Rwork0.229 ---
all-27881 --
obs-27384 98.2 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 171 2085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.22
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.1 Å2

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