1H2T

Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Large-Scale Induced Fit Recognition of an M(7)Gpppg CAP Analogue by the Human Nuclear CAP-Binding Complex

Mazza, C.Segref, A.Mattaj, I.W.Cusack, S.

(2002) Embo J. 21: 5548

  • Primary Citation of Related Structures:  1H2U, 1H2V

  • PubMed Abstract: 
  • The heterodimeric nuclear cap-binding complex (CBC) binds to the 5' cap structure of RNAs in the nucleus and plays a central role in their diverse maturation steps. We describe the crystal structure at 2.1 A resolution of human CBC bound to an m(7)Gp ...

    The heterodimeric nuclear cap-binding complex (CBC) binds to the 5' cap structure of RNAs in the nucleus and plays a central role in their diverse maturation steps. We describe the crystal structure at 2.1 A resolution of human CBC bound to an m(7)GpppG cap analogue. Comparison with the structure of uncomplexed CBC shows that cap binding induces co-operative folding around the dinucleotide of some 50 residues from the N- and C-terminal extensions to the central RNP domain of the small subunit CBP20. The cap-bound conformation of CBP20 is stabilized by an intricate network of interactions both to the ligand and within the subunit, as well as new interactions of the CBP20 N-terminal tail with the large subunit CBP80. Although the structure is very different from that of other known cap-binding proteins, such as the cytoplasmic cap-binding protein eIF4E, specificity for the methylated guanosine again is achieved by sandwiching the base between two aromatic residues, in this case two conserved tyrosines. Implications for the transfer of capped mRNAs to eIF4E, required for translation initiation, are discussed.


    Related Citations: 
    • Co-Crystallization of the Human Nuclear CAP-Binding Complex with a M7Gpppg CAP Analogue Using Protein Engineering
      Mazza, C.,Segref, A.,Mattaj, I.,Cusack, S.
      (2002) Acta Crystallogr.,Sect.D 58: 2194


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, c/o ILL, BP 181, F-38042 Grenoble cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
80 KDA NUCLEAR CAP BINDING PROTEIN
C
723Homo sapiensGene 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
Z
156Homo sapiensGene Names: NCBP2 (CBP20)
Find proteins for P52298 (Homo sapiens)
Go to Gene View: NCBP2
Go to UniProtKB:  P52298
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
Z
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
7MG
Query on 7MG

Download SDF File 
Download CCD File 
Z
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
C11 H18 N5 O8 P
ZMWJGXGSWZFZPJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.780α = 90.00
b = 112.780β = 90.00
c = 158.310γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-23
    Type: Data collection