Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 112483.91 
• Atom Count: 7361 
• Residue Count: 946 
• 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


• 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.Mol.Biol. 9: 912-917

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


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
80 kDa nuclear cap binding protein	A	790	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
20 kDa nuclear cap binding protein	B	156	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PG4	A	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GTG	B	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE MRNA CAP ANALOG N7-METHYL GPPPG C21 H30 N10 O18 P3 FHHZHGZBHYYWTG-INFSMZHSSA-O

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 = 90.00
b = 111.681	β = 90.00
c = 177.588	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance