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: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/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. 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
80 KDA NUCLEAR CAP BINDING PROTEINA [auth C]723Homo sapiensMutation(s): 1 
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
20 KDA NUCLEAR CAP BINDING PROTEINB [auth Z]156Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth Z]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
7MG
Query on 7MG

Download Ideal Coordinates CCD File 
D [auth Z]7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
C11 H18 N5 O8 P
ZMWJGXGSWZFZPJ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.78α = 90
b = 112.78β = 90
c = 158.31γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2017-08-23
    Changes: Data collection
  • Version 1.4: 2019-04-03
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description