Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.61 kDa 
• Atom Count: 1240 
• Modelled Residue Count: 156 
• Deposited Residue Count: 156 
• Unique protein chains: 2

2K8C

Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin

• PDB DOI: 10.2210/pdb2K8C/pdb

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


• Deposited: 2008-09-04 Released: 2009-05-05 
• Deposition Author(s): Fu, Q.S., Zhou, C.J., Gao, H.C., Lin, D.H., Hu, H.Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: 10 structures for lowest energy 

Literature

Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein.

Fu, Q.S., Zhou, C.J., Gao, H.C., Jiang, Y.J., Zhou, Z.R., Hong, J., Yao, W.M., Song, A.X., Lin, D.H., Hu, H.Y.

(2009) J Biol Chem 284: 19043-19052

• PubMed: 19423704 
• DOI: 10.1074/jbc.M109.009126
• Primary Citation of Related Structures:  
  2K89, 2K8A, 2K8B, 2K8C


• PubMed Abstract: 
  

Ubiquitin (Ub) is an essential modifier conserved in all eukaryotes from yeast to human. Phospholipase A(2)-activating protein (PLAA), a mammalian homolog of yeast DOA1/UFD3, has been proposed to be able to bind with Ub, which plays important roles in endoplasmic reticulum-associated degradation, vesicle formation, and DNA damage response. We have identified a core domain from the PLAA family ubiquitin-binding region of human PLAA (residues 386-465, namely PFUC) that can bind Ub and elucidated its solution structure and Ub-binding mode by NMR approaches. The PFUC domain possesses equal population of two conformers in solution by cis/trans-isomerization, whereas the two isomers exhibit almost equivalent Ub binding abilities. This domain structure takes a novel fold consisting of four beta-strands and two alpha-helices, and the Ub-binding site on PFUC locates in the surface of alpha2-helix, which is to some extent analogous to those of UBA, CUE, and UIM domains. This study provides structural basis and biochemical information for Ub recognition of the novel PFU domain from a PLAA family protein that may connect ubiquitination and degradation in endoplasmic reticulum-associated degradation.

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A-2-activating protein	B	80	Homo sapiens	Mutation(s): 0  Gene Names: PLAA, PLAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y263 (Homo sapiens) Explore Q9Y263  Go to UniProtKB:  Q9Y263
PHAROS:  Q9Y263

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: 10 structures for lowest energy 
• OLDERADO: 2K8C Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-04 
• Released Date: 2009-05-05 
Deposition Author(s): Fu, Q.S., Zhou, C.J., Gao, H.C., Lin, D.H., Hu, H.Y.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations