2Q8K | pdb_00002q8k

The crystal structure of Ebp1

• PDB DOI: https://doi.org/10.2210/pdb2Q8K/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-06-11 Released: 2007-09-25 
• Deposition Author(s): Kowalinski, E., Bange, G., Wild, K., Sinning, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.219 (Depositor) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of Ebp1 reveals a methionine aminopeptidase fold as binding platform for multiple interactions.

Kowalinski, E., Bange, G., Bradatsch, B., Hurt, E., Wild, K., Sinning, I.

(2007) FEBS Lett 581: 4450-4454

• PubMed: 17765895 
• DOI: https://doi.org/10.1016/j.febslet.2007.08.024
• Primary Citation Related Structures: 
  2Q8K


• PubMed Abstract: 
  

  The ErbB-3 receptor binding protein (Ebp1) is a member of the proliferation-associated 2G4 (PA2G4) family implicated in regulation of cell growth and differentiation. Here, we report the crystal structure of the human Ebp1 at 1.6 A resolution. The protein has the conserved pita bread fold of methionine aminopeptidases, but without the characteristic enzymatic activity. Moreover, Ebp1 is known to interact with a number of proteins and RNAs involved in either transcription regulation or translation control. The structure provides insights in how Ebp1 discriminates between its different interaction partners.

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Organizational Affiliation: 
• Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.4 kDa 
• Atom Count: 3,361 
• Modeled Residue Count: 354 
• Deposited Residue Count: 401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferation-associated protein 2G4	A	401	Homo sapiens	Mutation(s): 0  Gene Names: PA2G4, EBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ80 (Homo sapiens) Explore Q9UQ80  Go to UniProtKB:  Q9UQ80
PHAROS:  Q9UQ80 GTEx:  ENSG00000170515

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.219 (Depositor) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.887	α = 90
b = 73.887	β = 90
c = 183.348	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Kowalinski, E., Bange, G., Wild, K., Sinning, I.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description