1N52

Cap Binding Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.

Calero, G.Wilson, K.Ly, T.Rios-Steiner, J.Clardy, J.Cerione, R.

(2002) Nat.Struct.Mol.Biol. 9: 912-917

  • DOI: 10.1038/nsb874
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 7-methyl guanosine cap structure of RNA is essential for key aspects of RNA processing, including pre-mRNA splicing, 3' end formation, U snRNA transport, nonsense-mediated decay and translation. Two cap-binding proteins mediate these effects: cyt ...

    The 7-methyl guanosine cap structure of RNA is essential for key aspects of RNA processing, including pre-mRNA splicing, 3' end formation, U snRNA transport, nonsense-mediated decay and translation. Two cap-binding proteins mediate these effects: cytosolic eIF-4E and nuclear cap-binding protein complex (CBC). The latter consists of a CBP20 subunit, which binds the cap, and a CBP80 subunit, which ensures high-affinity cap binding. Here we report the 2.1 A resolution structure of human CBC with the cap analog m7GpppG, as well as the structure of unliganded CBC. Comparisons between these structures indicate that the cap induces substantial conformational changes within the N-terminal loop of CBP20, enabling Tyr 20 to join Tyr 43 in pi-pi stacking interactions with the methylated guanosine base. CBP80 stabilizes the movement of the N-terminal loop of CBP20 and locks the CBC into a high affinity cap-binding state. The structure for the CBC bound to m7GpppG highlights interesting similarities and differences between CBC and eIF-4E, and provides insights into the regulatory mechanisms used by growth factors and other extracellular stimuli to influence the cap-binding state of the CBC.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
80 kDa nuclear cap binding protein
A
790Homo sapiensMutation(s): 0 
Gene Names: NCBP1 (CBP80, NCBP)
Find proteins for Q09161 (Homo sapiens)
Go to Gene View: NCBP1
Go to UniProtKB:  Q09161
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
20 kDa nuclear cap binding protein
B
156Homo sapiensMutation(s): 0 
Gene Names: NCBP2 (CBP20)
Find proteins for P52298 (Homo sapiens)
Go to Gene View: NCBP2
Go to UniProtKB:  P52298
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
B
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
MRNA CAP ANALOG N7-METHYL GPPPG
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.681α = 90.00
b = 111.681β = 90.00
c = 177.588γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance