- PDB-3n1b: C-terminal domain of Vps54 subunit of the GARP complex -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3n1b
Title
C-terminal domain of Vps54 subunit of the GARP complex
Components
Vacuolar protein sorting-associated protein 54
Keywords
TRANSPORT PROTEIN / spinal muscular atrophy / vesicle trafficking / Golgi apparatus / tethering complex / GARP
Function / homology
Function and homology information
neural tissue regeneration / GARP complex / Retrograde transport at the Trans-Golgi-Network / post-embryonic forelimb morphogenesis / skeletal muscle tissue growth / vesicle-mediated cholesterol transport / musculoskeletal movement / thrombin-activated receptor signaling pathway / spermatid differentiation / L-glutamate import ...neural tissue regeneration / GARP complex / Retrograde transport at the Trans-Golgi-Network / post-embryonic forelimb morphogenesis / skeletal muscle tissue growth / vesicle-mediated cholesterol transport / musculoskeletal movement / thrombin-activated receptor signaling pathway / spermatid differentiation / L-glutamate import / sphingolipid catabolic process / ubiquitin recycling / Golgi to vacuole transport / neuromuscular synaptic transmission / limb morphogenesis / apoptotic DNA fragmentation / protein targeting to ER / cellular response to progesterone stimulus / neuroinflammatory response / protein targeting to vacuole / vacuole organization / protein targeting to lysosome / neurofilament cytoskeleton organization / microglia differentiation / astrocyte differentiation / negative regulation of motor neuron apoptotic process / protein localization to cell surface / retrograde transport, endosome to Golgi / synaptic transmission, GABAergic / regulation of growth / limb development / motor behavior / lysosomal transport / syntaxin binding / motor neuron apoptotic process / homeostasis of number of cells / striated muscle contraction / skeletal muscle tissue development / homeostasis of number of cells within a tissue / respiratory electron transport chain / neuron projection morphogenesis / mitochondrion organization / synaptic transmission, glutamatergic / trans-Golgi network / intracellular calcium ion homeostasis / response to calcium ion / protein localization / gene expression / neuron apoptotic process / in utero embryonic development / response to antibiotic / synapse / perinuclear region of cytoplasm / mitochondrion / nucleoplasm / membrane / cytosol / cytoplasm Similarity search - Function
Monooxygenase - #130 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #860 / Vacuolar protein sorting-associated protein 54, C-terminal / Vacuolar protein sorting-associated protein 54, N-terminal / Vacuolar protein sorting-associated protein 54 / Vps54-like protein / Vacuolar-sorting protein 54, of GARP complex / Monooxygenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Monooxygenase - #130 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #860 / Vacuolar protein sorting-associated protein 54, C-terminal / Vacuolar protein sorting-associated protein 54, N-terminal / Vacuolar protein sorting-associated protein 54 / Vps54-like protein / Vacuolar-sorting protein 54, of GARP complex / Monooxygenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
Density Matthews: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 23% PEG3350, 0.1M BisTris, 0.1M I3C, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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Data collection
Diffraction
ID
Crystal-ID
1
1
2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ESRF
ID23-1
1
1.7
SYNCHROTRON
ESRF
ID23-1
2
0.9791, 0.9794
Detector
Type
ID
Detector
ADSC QUANTUM 315r
1
CCD
ADSC QUANTUM 315r
2
CCD
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
MAD
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.7
1
2
0.9791
1
3
0.9794
1
Reflection
Redundancy: 6.3 % / Av σ(I) over netI: 12.34 / Number: 57298 / Rmerge(I) obs: 0.07 / Χ2: 1.02 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 9115 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
5.6
50
99.2
1
0.037
1.025
6.8
4.45
5.6
100
1
0.065
1.034
6.8
3.88
4.45
100
1
0.082
1.023
7
3.53
3.88
100
1
0.087
1.017
7
3.28
3.53
100
1
0.089
1.02
6.9
3.08
3.28
100
1
0.104
1.043
6.8
2.93
3.08
100
1
0.115
1.003
6.5
2.8
2.93
99.9
1
0.14
1.002
5.9
2.69
2.8
99.1
1
0.164
1.006
5.2
2.6
2.69
94.6
1
0.188
1.027
3.9
Reflection
Resolution: 2.398→50 Å / Num. obs: 11565 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Χ2: 1.035 / Net I/σ(I): 18.4
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