PDBsum entry: 1h6k

Nuclear protein

PDB-id: 1h6k

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Description

Header details

Header records

References

PROCHECK

Protein chains

728 a.a. *

77 a.a. *

78 a.a. *

Waters ×1710

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1h6k

Name:

Nuclear protein

Title:

Nuclear cap binding complex

Structure:

Cbp80. Chain: a, b, c. Fragment: mif4g domain. Synonym: ncbp 80 kda subunit, cbp80. Engineered: yes. Mutation: yes. 20 kda nuclear cap binding protein. Chain: x, y, z. Fragment: rnp domain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five. Other_details: expression in insect cells. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Biological unit:

Dimer (from PDB file)

UniProt:

Chains A, B, C: Q09161 (NCBP1_HUMAN)

Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:	790 a.a.
	Struc:	728 a.a.*

Chains X, Y: P52298 (NCBP2_HUMAN)

Seq:	156 a.a.
Struc:	77 a.a.

Chain Z: P52298 (NCBP2_HUMAN)

Seq:

156 a.a.

Struc:

78 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

2.00Å

R-factor:

0.203

R-free:

0.234

Authors:

C.Mazza,M.Ohno,A.Segref,I.W.Mattaj,S.Cusack

Key ref:

C.Mazza et al. (2001). Crystal structure of the human nuclear cap binding complex.. Mol Cell, 8, 383-396. [PubMed id: 11545740] [DOI: 10.1016/S1097-2765(01)00299-4]

Date:

18-Jun-01

Release date:

13-Sep-01

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Key reference

DOI no: 10.1016/S1097-2765(01)00299-4

Mol Cell 8:383-396 (2001)

PubMed id: 11545740

Crystal structure of the human nuclear cap binding complex.

C.Mazza, M.Ohno, A.Segref, I.W.Mattaj, S.Cusack.

ABSTRACT

The heterodimeric nuclear cap binding complex (CBC) binds to 5'-capped polymerase II transcripts. It enhances the efficiency of several mRNA maturation steps and is essential for U snRNA nuclear export in multicellular eukaryotes. The 2A crystal structure of human CBC shows that the large subunit, CBP80, comprises three domains, each containing consecutive helical hairpins and resembling the so-called MIF4G domain found in several other proteins involved in RNA metabolism. The small subunit, CPB20, has an RNP fold and associates with the second and third domains of CBP80. Site-directed mutagenesis revealed 4 residues of CBP20 which are critical for cap binding. A model for cap binding is proposed based on these results and the known mode of binding of RNA to RNP domains.

Selected figure(s)

Figure 3.
Figure 3. CBP80 Contains a Repeated Six-Helix Motif and a MIF4G Domain(A) Repeats 1, 2, and 3 corresponding to the N-terminal six helices of the CBP80 domains 1, 2, and 3. Structurally homologous domains identified by the program DALI are shown in the same orientation: the ENTH domain from Epsin 1 (Hyman et al., 2000) and the VHS domain from TOM1 (Misra et al., 2000). The face formed by the A1, A2, and A3 helices corresponds to the concave face and that formed by the B1, B2 and B3 helices, to the convex face. The figure was generated with BOBSCRIPT (Esnouf, 1999).(B) Structure-based alignment of the three six-helix motifs in CBP80 and the corresponding motif from the MIF4G domain of eIF4GII (Marcotrigiano et al., 2001). The homologies between repeats 1 and 2 and eIF4GII are highlighted in red and the conserved residues among all four structures are represented by yellow boxes. Identities are indicated with red boxes.(C) Stereodiagram showing the superposition of the MIF4G domains of CBP80 (residues 26–240, blue) and eIF4GII (residues 753–986, cyan). The DALI Z score for this superposition is 13.4. The N terminus is at the top.(D) Structure-based alignment of the MIF4G domains of CBP80 and eIF4GII. Identities are indicated by red boxes, and conservative substitutions by yellow boxes. Note that eIF4GII has a long linker between helices A3 and B3 (disordered in the crystal structure), whereas CBP80 has a long linker between A5 and B5

Figure 4.
Figure 4. Comparison of the CBP20 RNP Domain with PABP and Sxl(A) CBP20 RNP domain (residues 38–118, green). The trypsin cut between Lys-77 and Cys-81 is represented with a green dashed line. The observed conformation of the peptide 72–77, which is stabilized by a salt bridge between residues Lys-75 and Asp-116 and certain side chains are shown in gold. A presumed native-like conformation of the loop 72–81 and conformations of Tyr-43 and Phe-83, modeled from the PABP structure shown in (B), are depicted in blue.(B) The N-terminal domain of poly (A) binding protein (residues 11–94, red) complexed with poly (A) (gray backbone, cyan bases). The three aromatic residues from RNP1 (Tyr-54 and Tyr-56) and RNP2 (Tyr-14) are shown in blue.(C) The second RNP domain of Sxl (residues 206–289, yellow) in complex with cognate RNA. Color scheme as in (B)

The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 383-396) copyright 2001.

Figures were selected by the author.