1H2V

Structure of the human nuclear cap-binding-complex (CBC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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

  • DOI: 10.1093/emboj/cdf538
  • Primary Citation of Related Structures:  
    1H2T, 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)GpppG cap analogue ...

    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 D Biol Crystallogr 58: 2194
    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
80 KDA NUCLEAR CAP BINDING PROTEINA [auth C]771Homo sapiensMutation(s): 1 
Gene Names: NCBP1, CBP80, NCBP
UniProt & NIH Common Fund Data Resources
Find proteins for Q09161 (Homo sapiens)
Explore Q09161 
Go to UniProtKB:  Q09161
PHAROS:  Q09161
GTEx:  ENSG00000136937 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09161
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
20 KDA NUCLEAR CAP BINDING PROTEINB [auth Z]156Homo sapiensMutation(s): 0 
Gene Names: NCBP2, CBP20, PIG55
UniProt & NIH Common Fund Data Resources
Find proteins for P52298 (Homo sapiens)
Explore P52298 
Go to UniProtKB:  P52298
PHAROS:  P52298
GTEx:  ENSG00000114503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52298
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.136α = 90
b = 59.605β = 99.52
c = 75.43γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy