[English] 日本語
Yorodumi
- PDB-3n1e: Vps54 C-terminal domain -

+
Open data


ID or keywords:

Loading...

-
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 / motor neuron apoptotic process / musculoskeletal movement / skeletal muscle tissue growth / neural tissue regeneration ...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 / motor neuron apoptotic process / musculoskeletal movement / skeletal muscle tissue growth / neural tissue regeneration / limb morphogenesis / L-glutamate import / cellular response to progesterone stimulus / ubiquitin recycling / microglia differentiation / neuroinflammatory response / neuromuscular synaptic transmission / apoptotic DNA fragmentation / protein targeting to ER / vacuole organization / neurofilament cytoskeleton organization / Golgi to vacuole transport / protein targeting to lysosome / protein targeting to vacuole / astrocyte differentiation / sphingolipid catabolic process / motor behavior / regulation of growth / protein localization to cell surface / retrograde transport, endosome to Golgi / lysosomal transport / syntaxin binding / thrombin-activated receptor signaling pathway / synaptic transmission, GABAergic / homeostasis of number of cells / limb development / skeletal muscle tissue development / homeostasis of number of cells within a tissue / neuron projection morphogenesis / mitochondrion organization / striated muscle contraction / respiratory electron transport chain / trans-Golgi network / synaptic transmission, glutamatergic / response to calcium ion / intracellular calcium ion homeostasis / gene expression / in utero embryonic development / intracellular protein localization / neuron apoptotic process / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more