Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.48 kDa 
• Atom Count: 7699 
• Residue Count: 880 
• Unique protein chains: 2

1N52

Cap Binding Complex

• DOI: 10.2210/pdb1N52/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-11-04 Released: 2003-02-18 
• Deposition Author(s): Calero, G., Wilson, K., Ly, T., Rios-Steiner, J., Clardy, J., Cerione, R.

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Experimental Data Snapshot

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

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 Biol 9: 912-917

• PubMed: 12434151 
• DOI: 10.1038/nsb874
• Primary Citation of Related Structures:  
  1N54, 1N52


• 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: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
80 kDa nuclear cap binding protein	A	790	Homo sapiens	Mutation(s): 0  Gene Names: CBP80, NCBP1, NCBP
Find proteins for Q09161 (Homo sapiens) Explore Q09161  Go to UniProtKB:  Q09161
NIH Common Fund Data Resources
PHAROS  Q09161 GTEx  ENSG00000136937

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
20 kDa nuclear cap binding protein	B	156	Homo sapiens	Mutation(s): 0  Gene Names: CBP20, NCBP2, PIG55
Find proteins for P52298 (Homo sapiens) Explore P52298  Go to UniProtKB:  P52298
NIH Common Fund Data Resources
PHAROS  P52298 GTEx  ENSG00000114503

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTG	B	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE C21 H30 N10 O18 P3 FHHZHGZBHYYWTG-INFSMZHSSA-O
PG4	A	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 111.681	α = 90
b = 111.681	β = 90
c = 177.588	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-04 
• Released Date: 2003-02-18 
Deposition Author(s): Calero, G., Wilson, K., Ly, T., Rios-Steiner, J., Clardy, J., Cerione, R.

Revision History 

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