PDBsum entry 1n54

RNA binding protein

PDB id: 1n54

Contents

Protein chains

733 a.a. *

121 a.a. *

Ligands

GOL ×7

Waters ×255

* Residue conservation analysis

PDB id:

1n54

Name:

RNA binding protein

Title:

Cap binding complex m7gpppg free

Structure:

80 kda nuclear cap binding protein. Chain: a. Synonym: ncbp 80 kda subunit, cap binding protein 80, cbp80. Engineered: yes. 20 kda nuclear cap binding protein. Chain: b. Synonym: ncbp 20 kda subunit, cap binding protein 20, cbp20, ncbp interacting protein 1, nip1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cbp80. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf21. Gene: cbp20.

Biol. unit:

Dimer (from PQS)

Resolution:

2.72Å R-factor: 0.263 R-free: 0.282

Authors:

G.Calero,K.Wilson,T.Ly,J.Rios-Steiner,J.Clardy,R.Cerione

Key ref:

G.Calero et al. (2002). Structural basis of m7GpppG binding to the nuclear cap-binding protein complex. Nat Struct Biol, 9, 912-917. PubMed id: 12434151 DOI: 10.1038/nsb874

Date:

04-Nov-02 Release date: 18-Feb-03

Protein chain

Q09161  (NCBP1_HUMAN) -  Nuclear cap-binding protein subunit 1 from Homo sapiens

Seq: 790 a.a.

Struc: 733 a.a.

Protein chain

P52298  (NCBP2_HUMAN) -  Nuclear cap-binding protein subunit 2 from Homo sapiens

Seq: 156 a.a.

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1038/nsb874

Nat Struct Biol 9:912-917 (2002)

PubMed id: 12434151

Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.

G.Calero, K.F.Wilson, T.Ly, J.L.Rios-Steiner, J.C.Clardy, R.A.Cerione.

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.

Selected figure(s)

Figure 2.
Figure 2. Interactions of CBP20 with m7GpppG. a, Stereo depiction of the electron density (2F[o] - F[c]) simulated annealing omit map calculated omitting m7GpppG and contoured at 3.0 . The average B-factors for 7-methylated guanosine triphosphate and the nonmethylated guanosine are 45 Å2 and 79 Å2, respectively. b, Surface electrostatic representation calculated with SPOCK (http://quorum.tamu.edu/spock/) for the m7GpppG-binding cavity. The roof and part of the floor of the cavity are formed by residues Tyr 20 and Tyr 43, respectively. The electrostatic potential inside the cavity neutralizes the charges of the guanosine base and the phosphate oxygen atoms. c, Ball-and-stick representation of - stacking and degree of overlap between Tyr 20, m7GpppG and Tyr 43. Tyr 20 makes two hydrogen bonds with 7-methyl guanosine: Tyr 20(OH) -O1B = 2.81 Å and Tyr 20(OH) -O2 = 2.95 Å (see text). The left and the right depictions are related by a 90° rotation along the plane perpendicular to the page. d, Schematic representation using LigplOt36 of the hydrogen bond network stabilizing m7GpppG. Residue color is N-terminus (magenta), RNP domain (gray) and C-terminus (green). Red arches indicate residues involved in van der Waals contacts. Numbers indicate distances in (Å).

Figure 4.
Figure 4. Surface (CBP80) and ribbon (CBP20) representation of the CBC to illustrate the stabilization of the N-terminal hinge of CBP20 by CBP80. The N-terminal region of CBP20 (residues Ser 11, Asp 12 and Ser 13 shown in magenta) crosses through a 'binding grove' formed by residues Lys 327 and Glu 328 of CBP80 (cyan), making several contacts that allow the hinged motion of residues 16 -29 of CBP20 in loop 2 - 3. The N-terminal region of CBP80 is blue. The inset shows these interactions in detail, including the hydrogen bonds Lys 327(NZ) -Leu 9(O) = 3.3 Å, Glu 328(OE2) -Ser 11(OG) = 2.93 Å and Glu 328(OE2) -Ser 13(N) = 2.74 Å.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 912-917) copyright 2002.

Figures were selected by an automated process.