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- PDB-1u5t: Structure of the ESCRT-II endosomal trafficking complex -

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Basic information

Entry
Database: PDB / ID: 1u5t
TitleStructure of the ESCRT-II endosomal trafficking complex
Components
  • Defective in vacuolar protein sorting; Vps36p
  • Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
  • appears to be functionally related to SNF7; Snf8p
KeywordsTRANSPORT PROTEIN / escrt / endosomal / trafficking / protein complex
Function / homology
Function and homology information


ESCRT II complex / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / ubiquitin binding ...ESCRT II complex / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / ubiquitin binding / macroautophagy / late endosome membrane / lipid binding / structural molecule activity / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
Helix Hairpins - #180 / ESCRT-2 complex, Snf8 / Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain / Vacuolar protein sorting 36 NZF-N zinc-finger domain / "Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 ...Helix Hairpins - #180 / ESCRT-2 complex, Snf8 / Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain / Vacuolar protein sorting 36 NZF-N zinc-finger domain / "Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Zinc finger domain / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein-sorting-associated protein 25 / Vacuolar protein-sorting-associated protein 36 / Vacuolar-sorting protein SNF8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.6 Å
AuthorsHierro, A. / Sun, J. / Rusnak, A.S. / Kim, J. / Prag, G. / Emr, S.D. / Hurley, J.H.
Citation
Journal: Nature / Year: 2004
Title: Structure of ESCRT-II endosomal trafficking complex
Authors: Hierro, A. / Sun, J. / Rusnak, A.S. / Kim, J. / Prag, G. / Emr, S.D. / Hurley, J.H.
#1: Journal: DEV.CELL / Year: 2004
Title: ESCRT-II, an endosome-associated complex required for protein sorting: Crystal structure and interactions with ESCRT-III and membranes
Authors: Teo, H. / Perisic, O. / Gonzalez, B. / Williams, R.L.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: appears to be functionally related to SNF7; Snf8p
B: Defective in vacuolar protein sorting; Vps36p
C: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
D: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region


Theoretical massNumber of molelcules
Total (without water)93,8114
Polymers93,8114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.040, 150.040, 185.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein appears to be functionally related to SNF7; Snf8p


Mass: 26988.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pST39 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12483
#2: Protein Defective in vacuolar protein sorting; Vps36p


Mass: 19657.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pST39 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q06696
#3: Protein Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region


Mass: 23582.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pST39 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P47142

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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: 5.57 Å3/Da / Density % sol: 77.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Naacetate, hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DetectorDate: Feb 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.6→6 Å / Num. all: 44800 / Num. obs: 41210 / % possible obs: 91.9 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 3.6→6 Å
RfactorNum. reflection
Rfree0.2885 4013
Rwork0.2259 -
all0.2362 44800
obs0.2362 41210
Refinement stepCycle: LAST / Resolution: 3.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 0 0 6055
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.165
X-RAY DIFFRACTIONc_angle_deg2.557
X-RAY DIFFRACTIONc_mcbond_it9.3295
X-RAY DIFFRACTIONc_scbond_it18.17810
X-RAY DIFFRACTIONc_mcangle_it15.43610
X-RAY DIFFRACTIONc_scangle_it25.15415

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