Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 19.70 kDa 
• Atom Count: 1481 
• Modelled Residue Count: 173 
• Deposited Residue Count: 174 
• Unique protein chains: 1

1E7Z

Crystal structure of the EMAP2/RNA binding domain of the p43 protein from human aminoacyl-tRNA synthetase complex

• PDB DOI: 10.2210/pdb1E7Z/pdb

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


• Deposited: 2000-09-13 Released: 2000-11-27 
• Deposition Author(s): Pasqualato, S., Kerjan, P., Renault, L., Menetrey, J., Mirande, M., Cherfils, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.272 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Structure of the Emapii Domain of Human Aminoacyl-tRNA Synthetase Complex Reveals Evolutionary Dimeric Mimicry

Renault, L., Kerjan, P., Pasqualato, S., Menetrey, J., Robinson, J.C., Kawaguchi, S., Vassylyev, D.G., Yokoyama, S., Mirande, M., Cherfils, J.

(2001) EMBO J 20: 570

• PubMed: 11157763 
• DOI: 10.1093/emboj/20.3.570
• Primary Citation of Related Structures:  
  1E7Z, 1FL0


• PubMed Abstract: 
  

The EMAPII (endothelial monocyte-activating polypeptide II) domain is a tRNA-binding domain associated with several aminoacyl-tRNA synthetases, which becomes an independent domain with inflammatory cytokine activity upon apoptotic cleavage from the p43 component of the multisynthetase complex. It comprises a domain that is highly homologous to bacterial tRNA-binding proteins (Trbp), followed by an extra domain without homology to known proteins. Trbps, which may represent ancient tRNA chaperones, form dimers and bind one tRNA per dimer. In contrast, EMAPII domains are monomers. Here we report the crystal structure at 1.14 Angstroms of human EMAPII. The structure reveals that the Trbp-like domain, which forms an oligonucleotide-binding (OB) fold, is related by degenerate 2-fold symmetry to the extra-domain. The pseudo-axis coincides with the dyad axis of bacterial TtCsaA, a Trbp whose structure was solved recently. The interdomain interface in EMAPII mimics the intersubunit interface in TtCsaA, and may thus generate a novel OB-fold-based tRNA-binding site. The low sequence homology between the extra domain of EMAPII and either its own OB fold or that of Trbps suggests that dimer mimicry originated from convergent evolution rather than gene duplication.

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 1 Avenue de la Terrasse, 91198 Gif sur Yvette cedex, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II	A	174	Homo sapiens	Mutation(s): 0  Gene Names: AIMP1, EMAP2, SCYE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12904 (Homo sapiens) Explore Q12904  Go to UniProtKB:  Q12904
PHAROS:  Q12904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A], C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.272 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.141	α = 90
b = 53.938	β = 111.92
c = 41.371	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
TRUNCATE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-09-13 
• Released Date: 2000-11-27 
Deposition Author(s): Pasqualato, S., Kerjan, P., Renault, L., Menetrey, J., Mirande, M., Cherfils, J.

Revision History  

• Version 1.0: 2000-11-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance