5ZC9

Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.

Iwasaki, S.Iwasaki, W.Takahashi, M.Sakamoto, A.Watanabe, C.Shichino, Y.Floor, S.N.Fujiwara, K.Mito, M.Dodo, K.Sodeoka, M.Imataka, H.Honma, T.Fukuzawa, K.Ito, T.Ingolia, N.T.

(2018) Mol. Cell --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic initiation factor 4A-I
A
394Homo sapiensMutation(s): 0 
Gene Names: EIF4A1 (DDX2A, EIF4A)
EC: 3.6.4.13
Find proteins for P60842 (Homo sapiens)
Go to Gene View: EIF4A1
Go to UniProtKB:  P60842
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')B10synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
RCG
Query on RCG

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Download CCD File 
B
(1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide
Rocaglamide, Rocaglamide A
C29 H31 N O7
DAPAQENNNINUPW-IDAMAFBJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.508α = 90.00
b = 100.263β = 90.00
c = 155.422γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release