2HTH | pdb_00002hth

Structural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain

• PDB DOI: https://doi.org/10.2210/pdb2HTH/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-25 Released: 2006-10-24 
• Deposition Author(s): Alam, S.L., Whitby, F.G., Hill, C.P., Sundquist, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.289 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain.

Alam, S.L., Langelier, C., Whitby, F.G., Koirala, S., Robinson, H., Hill, C.P., Sundquist, W.I.

(2006) Nat Struct Mol Biol 13: 1029-1030

• PubMed: 17057716 
• DOI: https://doi.org/10.1038/nsmb1160
• Primary Citation Related Structures: 
  2HTH


• PubMed Abstract: 
  

  The ESCRT-I and ESCRT-II complexes help sort ubiquitinated proteins into vesicles that accumulate within multivesicular bodies (MVBs). Crystallographic and biochemical analyses reveal that the GLUE domain of the human ESCRT-II EAP45 (also called VPS36) subunit is a split pleckstrin-homology domain that binds ubiquitin along one edge of the beta-sandwich. The structure suggests how human ESCRT-II can couple recognition of ubiquitinated cargoes and endosomal phospholipids during MVB protein sorting.

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Organizational Affiliation: 
• Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.83 kDa 
• Atom Count: 1,640 
• Modeled Residue Count: 202 
• Deposited Residue Count: 216 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA52, UBB, UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting protein 36	B	140	Homo sapiens	Mutation(s): 0  Gene Names: VPS36, C13orf9, EAP45
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VN1 (Homo sapiens) Explore Q86VN1  Go to UniProtKB:  Q86VN1
PHAROS:  Q86VN1 GTEx:  ENSG00000136100

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.289 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.727	α = 90
b = 102.727	β = 90
c = 54.306	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-24 
Deposition Author(s): Alam, S.L., Whitby, F.G., Hill, C.P., Sundquist, W.I.

Revision History  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2024-02-14
  Changes: Advisory, Data collection, Database references