1XB4

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II

• PDB DOI: https://doi.org/10.2210/pdb1XB4/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-27 Released: 2005-03-22 
• Deposition Author(s): Weissenhorn, W., Wernimont, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.327 
• R-Value Work: 0.327 
• R-Value Observed: 0.273 

Literature

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II.

Wernimont, A.K., Weissenhorn, W.

(2004) BMC Struct Biol 4: 10-10

• PubMed: 15579210 
• DOI: https://doi.org/10.1186/1472-6807-4-10
• Primary Citation of Related Structures:  
  1XB4


• PubMed Abstract: 
  

  Down-regulation of plasma membrane receptors via the endocytic pathway involves their monoubiquitylation, transport to endosomal membranes and eventual sorting into multi vesicular bodies (MVB) destined for lysosomal degradation. Successive assemblies of Endosomal Sorting Complexes Required for Transport (ESCRT-I, -II and III) largely mediate sorting of plasma membrane receptors at endosomal membranes, the formation of multivesicular bodies and their release into the endosomal lumen. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Grenoble, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.33 kDa 
• Atom Count: 5,773 
• Modelled Residue Count: 693 
• Deposited Residue Count: 808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region	A, B, C, D	202	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YJR102C, J1957
UniProt
Find proteins for P47142 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47142  Go to UniProtKB:  P47142

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.327 
• R-Value Work: 0.327 
• R-Value Observed: 0.273 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.36	α = 90
b = 123.66	β = 90
c = 140.3	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
XDS	data reduction
SOLVE	phasing
CNS	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-22 
Deposition Author(s): Weissenhorn, W., Wernimont, A.K.

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references