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- PDB-3n1e: Vps54 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3n1e
TitleVps54 C-terminal domain
ComponentsVacuolar protein sorting-associated protein 54
KeywordsTRANSPORT PROTEIN / spinal muscular atrophy / vesicle trafficking / Golgi apparatus / tethering complex / GARP.
Function / homology
Function and homology information


post-embryonic forelimb morphogenesis / GARP complex / Retrograde transport at the Trans-Golgi-Network / negative regulation of motor neuron apoptotic process / spermatid differentiation / vesicle-mediated cholesterol transport / neural tissue regeneration / musculoskeletal movement / skeletal muscle tissue growth / limb morphogenesis ...post-embryonic forelimb morphogenesis / GARP complex / Retrograde transport at the Trans-Golgi-Network / negative regulation of motor neuron apoptotic process / spermatid differentiation / vesicle-mediated cholesterol transport / neural tissue regeneration / musculoskeletal movement / skeletal muscle tissue growth / limb morphogenesis / L-glutamate import / cellular response to progesterone stimulus / motor neuron apoptotic process / ubiquitin recycling / microglia differentiation / vacuole organization / neuroinflammatory response / apoptotic DNA fragmentation / homeostasis of number of cells / protein targeting to ER / neuromuscular synaptic transmission / neurofilament cytoskeleton organization / regulation of growth / Golgi to vacuole transport / protein targeting to lysosome / protein targeting to vacuole / astrocyte differentiation / homeostasis of number of cells within a tissue / sphingolipid catabolic process / protein localization to cell surface / motor behavior / syntaxin binding / retrograde transport, endosome to Golgi / lysosomal transport / skeletal muscle tissue development / thrombin-activated receptor signaling pathway / synaptic transmission, GABAergic / limb development / neuron apoptotic process / in utero embryonic development / neuron projection morphogenesis / gene expression / respiratory electron transport chain / mitochondrion organization / striated muscle contraction / synaptic transmission, glutamatergic / trans-Golgi network / response to calcium ion / intracellular calcium ion homeostasis / intracellular protein localization / response to antibiotic / synapse / perinuclear region of cytoplasm / Golgi apparatus / 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 / MOLECULAR REPLACEMENT / Resolution: 1.702 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 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,02011
Polymers32,5302
Non-polymers4909
Water5,945330
1
A: Vacuolar protein sorting-associated protein 54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5655
Polymers16,2651
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4546
Polymers16,2651
Non-polymers1895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Vacuolar protein sorting-associated protein 54
hetero molecules

B: Vacuolar protein sorting-associated protein 54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,02011
Polymers32,5302
Non-polymers4909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area2990 Å2
ΔGint-30 kcal/mol
Surface area14700 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-12 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.760, 77.064, 120.057
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16264.862 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% PEG3350, 0.2M MgCl2, 5% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30991 / % possible obs: 99 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.063 / Χ2: 1.019 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.766.80.4529781.01196
1.76-1.8370.34129751.02497.6
1.83-1.917.10.25230191.01498.9
1.91-2.027.10.16530611.07999.1
2.02-2.147.20.11230761.05499.4
2.14-2.317.20.0931081.00299.8
2.31-2.547.30.0730811.00299.8
2.54-2.917.50.06131391.0199.8
2.91-3.667.90.05531911.005100
3.66-507.60.02833630.99799.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→47.357 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.875 / SU ML: 0.2 / σ(F): 0.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1514 5.05 %
Rwork0.176 --
obs0.178 29964 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.976 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 79.12 Å2 / Biso mean: 20.959 Å2 / Biso min: 4.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.815 Å2-0 Å2-0 Å2
2---0.987 Å20 Å2
3----2.828 Å2
Refinement stepCycle: LAST / Resolution: 1.702→47.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 29 330 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122444
X-RAY DIFFRACTIONf_angle_d1.2843319
X-RAY DIFFRACTIONf_chiral_restr0.086371
X-RAY DIFFRACTIONf_plane_restr0.006419
X-RAY DIFFRACTIONf_dihedral_angle_d18.356944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.702-1.7570.2391150.2022285240085
1.757-1.820.2251220.1842355247790
1.82-1.8930.2391190.1812472259193
1.893-1.9790.1921280.1692541266995
1.979-2.0830.2011520.1642538269097
2.083-2.2140.2061330.1622611274498
2.214-2.3840.2181440.172637278199
2.384-2.6240.2141450.1782666281199
2.624-3.0040.2061470.17727122859100
3.004-3.7840.1971550.16327302885100
3.784-47.3750.2141540.18129033057100

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