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- PDB-3n1b: C-terminal domain of Vps54 subunit of the GARP complex -

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Basic information

Entry
Database: PDB / ID: 3n1b
TitleC-terminal domain of Vps54 subunit of the GARP complex
ComponentsVacuolar protein sorting-associated protein 54
KeywordsTRANSPORT PROTEIN / spinal muscular atrophy / vesicle trafficking / Golgi apparatus / tethering complex / GARP
Function / homology
Function and homology information


GARP complex / neural tissue regeneration / Retrograde transport at the Trans-Golgi-Network / post-embryonic forelimb morphogenesis / vesicle-mediated cholesterol transport / skeletal muscle tissue growth / spermatid differentiation / musculoskeletal movement / L-glutamate import / ubiquitin recycling ...GARP complex / neural tissue regeneration / Retrograde transport at the Trans-Golgi-Network / post-embryonic forelimb morphogenesis / vesicle-mediated cholesterol transport / skeletal muscle tissue growth / spermatid differentiation / musculoskeletal movement / L-glutamate import / ubiquitin recycling / apoptotic DNA fragmentation / protein targeting to ER / limb morphogenesis / cellular response to progesterone stimulus / neuroinflammatory response / vacuole organization / neurofilament cytoskeleton organization / neuromuscular synaptic transmission / protein targeting to vacuole / protein targeting to lysosome / microglia differentiation / astrocyte differentiation / negative regulation of motor neuron apoptotic process / sphingolipid catabolic process / retrograde transport, endosome to Golgi / protein localization to cell surface / regulation of growth / limb development / motor neuron apoptotic process / lysosomal transport / motor behavior / synaptic transmission, GABAergic / thrombin-activated receptor signaling pathway / homeostasis of number of cells / striated muscle contraction / skeletal muscle tissue development / homeostasis of number of cells within a tissue / neuron projection morphogenesis / respiratory electron transport chain / synaptic transmission, glutamatergic / mitochondrion organization / trans-Golgi network / intracellular calcium ion homeostasis / response to calcium ion / intracellular protein localization / neuron apoptotic process / gene expression / 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
Vacuolar protein sorting-associated protein 54
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.398 Å
AuthorsPerez-Victoria, F.J. / Abascal-Palacios, G. / Tascon, I. / Kajava, A. / Pioro, E.P. / Bonifacino, J.S. / Hierro, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex.
Authors: Perez-Victoria, F.J. / Abascal-Palacios, G. / Tascon, I. / Kajava, A. / Magadan, J.G. / Pioro, E.P. / Bonifacino, J.S. / Hierro, A.
History
DepositionMay 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 54
B: Vacuolar protein sorting-associated protein 54


Theoretical massNumber of molelcules
Total (without water)32,9992
Polymers32,9992
Non-polymers00
Water1,13563
1
A: Vacuolar protein sorting-associated protein 54


Theoretical massNumber of molelcules
Total (without water)16,4991
Polymers16,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 54


Theoretical massNumber of molelcules
Total (without water)16,4991
Polymers16,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Vacuolar protein sorting-associated protein 54

B: Vacuolar protein sorting-associated protein 54


Theoretical massNumber of molelcules
Total (without water)32,9992
Polymers32,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area1420 Å2
ΔGint-16 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.862, 30.323, 88.953
Angle α, β, γ (deg.)90.000, 120.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vacuolar protein sorting-associated protein 54 / Tumor antigen SLP-8p homolog


Mass: 16499.338 Da / Num. of mol.: 2 / Fragment: residues 836-974
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps54 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SPW0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 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
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.7
SYNCHROTRONESRF ID23-120.9791, 0.9794
Detector
TypeIDDetector
ADSC QUANTUM 315r1CCD
ADSC QUANTUM 315r2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.71
20.97911
30.97941
ReflectionRedundancy: 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 (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.210.0371.0256.8
4.455.610010.0651.0346.8
3.884.4510010.0821.0237
3.533.8810010.0871.0177
3.283.5310010.0891.026.9
3.083.2810010.1041.0436.8
2.933.0810010.1151.0036.5
2.82.9399.910.141.0025.9
2.692.899.110.1641.0065.2
2.62.6994.610.1881.0273.9
ReflectionResolution: 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
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.492.30.210431.04490.3
2.49-2.592.70.16811271.0496.7
2.59-2.73.10.12711391.0498.9
2.7-2.853.30.09911511.03699.8
2.85-3.023.50.08311711.03999.9
3.02-3.263.60.0711611.02999.9
3.26-3.583.60.05611621.01799.9
3.58-4.13.60.05611861.041100
4.1-5.173.50.06811951.038100
5.17-503.30.06112301.03698.6

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Phasing

Phasing dmFOM : 0.62 / FOM acentric: 0.63 / FOM centric: 0.59 / Reflection: 11554 / Reflection acentric: 10298 / Reflection centric: 1256
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-30.9760.930.950.85540396144
4.3-6.90.910.930.8115841334250
3.4-4.30.870.890.7519811748233
3-3.40.750.760.5919671773194
2.6-30.480.490.3834703166304
2.4-2.60.20.20.1320121881131

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
HKL-2000data reduction
HKL-2000data scaling
CRANKphasing
RefinementMethod to determine structure: MAD / Resolution: 2.398→30.976 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.786 / SU ML: 0.33 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 536 4.75 %
Rwork0.239 --
obs0.241 11296 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.967 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 124.91 Å2 / Biso mean: 50.553 Å2 / Biso min: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.804 Å2-0 Å2-0.488 Å2
2---1.056 Å20 Å2
3----0.749 Å2
Refinement stepCycle: LAST / Resolution: 2.398→30.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 0 63 2166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022146
X-RAY DIFFRACTIONf_angle_d0.5472898
X-RAY DIFFRACTIONf_chiral_restr0.038329
X-RAY DIFFRACTIONf_plane_restr0.002368
X-RAY DIFFRACTIONf_dihedral_angle_d15.087795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.398-2.640.3341300.2742411254188
2.64-3.0210.3061490.2542700284997
3.021-3.8060.281180.2322784290299
3.806-30.9780.2671390.2232865300499

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