2HYI

Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA

Structural Biology Knowledgebase: 2HYI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2HYI

Classification: hydrolase / RNA binding protein / RNA

Total Structure Weight: 172984.31


Macromolecule Entities
Molecule Chains Length Organism Details
Protein mago nashi homolog A, G 146 Homo sapiens Gene Name(s): MAGOH Gene View MAGOHA
RNA-binding protein 8A B, H 91 Homo sapiens Fragment: N-terminal deletion mutant
Gene Name(s): RBM8A Gene View RBM8 HSPC114 MDS014
Probable ATP-dependent RNA helicase DDX48 C, I 413 Homo sapiens EC#: 3.6.4.13 IUBMB
Gene Name(s): EIF4A3 Gene View DDX48 KIAA0111
Protein CASC3 D, J 77 Homo sapiens Fragment: Selor fragment
Gene Name(s): CASC3 Gene View MLN51
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*UP*UP*UP*UP*UP*U)-3' F, L 6 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ANP
Query on ANP

C, I PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

C, I MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.212
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 185.83 α = 90.00
b = 88.26 β = 110.77
c = 145.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-06
  • Released Date: 2006-08-15
  • Deposition author(s): Andersen, C.B.F., Le Hir, H., Andersen, G.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4