PDBsum entry: 1m8y

RNA binding protein/RNA

PDB-id: 1m8y

Asymmetric unit

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Description

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References

PROCHECK

Protein chains

341 a.a. *

DNA/RNA

Waters ×340

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1m8y

Name:

RNA binding protein/RNA

Title:

Crystal structure of the pumilio-homology domain from human pumilio1 in complex with nre2-10 RNA

Structure:

5'-r(p Ap Up Up Gp Up Ap Cp Ap Up A)-3'. Chain: c, d. Engineered: yes. Pumilio 1. Chain: a, b. Fragment: pumilio-homology domain, residues 828-1176. Engineered: yes

Source:

Synthetic: yes. Other_details: this sequence occurs naturally in drosophila melanogaster. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: Q14671 (PUM1_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1186 a.a.

Struc:

341 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

Resolution:

2.60Å

R-factor:

0.214

R-free:

0.286

Authors:

X.Wang,J.Mclachlan,P.D.Zamore,T.M.T.Hall

Key ref:

X.Wang et al. (2002). Modular recognition of RNA by a human pumilio-homology domain.. Cell, 110, 501-512. [PubMed id: 12202039] [DOI: 10.1016/S0092-8674(02)00873-5]

Date:

26-Jul-02

Release date:

25-Sep-02

Related entries:

1ib3
crystal structure of a pumilio-homology domain
1ib2
crystal structure of a pumilio-homology domain
1m8w
crystal structure of the pumilio-homology domain from human
pumilio1 in complex with nre1-14 RNA
1m8x
crystal structure of the pumilio-homology domain from human
pumilio1 in complex with nre1-14 RNA

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Clefts

Surface

Key reference

DOI no: 10.1016/S0092-8674(02)00873-5

Cell 110:501-512 (2002)

PubMed id: 12202039

Modular recognition of RNA by a human pumilio-homology domain.

X.Wang, J.McLachlan, P.D.Zamore, T.M.Hall.

ABSTRACT

Puf proteins are developmental regulators that control mRNA stability and translation by binding sequences in the 3' untranslated regions of their target mRNAs. We have determined the structure of the RNA binding domain of the human Puf protein, Pumilio1, bound to a high-affinity RNA ligand. The RNA binds the concave surface of the molecule, where each of the protein's eight repeats makes contacts with a different RNA base via three amino acid side chains at conserved positions. We have mutated these three side chains in one repeat, thereby altering the sequence specificity of Pumilio1. Thus, the high affinity and specificity of the PUM-HD for RNA is achieved using multiple copies of a simple repeated motif.

Selected figure(s)

Figure 2.
Figure 2. Protein:RNA Interactions(A) Sequence alignment of residues in the α helices of repeats 1–8 that line the inner concave surface of HsPUM-HD. The amino acid position number in the PUM repeats is shown above the alignment. Residues at position 13 that make stacking interactions with the RNA bases are highlighted magenta, residues at position 12 that make hydrogen bond (repeats 2, 6, 7, and 8) or van der Waals (repeats 1, 3, and 5) interactions are highlighted green, and residues at position 16 that make hydrogen bond interactions are highlighted light blue. Residues at position 10 that make van der Waals contacts with the ribose rings are highlighted orange, and residues at positions 17 and 20 that form an electrostatic network along with Glu-1083 at position 16 in repeat 7 are highlighted red (acidic) and blue (basic).(B) Schematic representation of protein:RNA contacts. The interactions observed in the structure of the HsPUM-HD:NRE2-10 complex are shown. Residues at positions 12, 13, and 16 are colored as in (A). Hydrogen bonds are indicated with dotted lines, stacking interactions are indicated with dashed lines, and van der Waals interactions are indicated with “))))))).” Distances in angstrom between atoms are indicated on the lines.

Figure 4.
Figure 4. Recognition of Uracil and Adenine Residues(A) Interaction of repeat 8 with Ura-3B. Tyr-1123 at position 13 in repeat 8 and His-1159 from repeat 8′ form stacking interactions with the uracil base. Asn-1122 (green) and Gln-1126 (blue) make hydrogen bonds with the uracil base. Hydrogen bonds are indicated with red dotted lines.(B) Interaction of repeats 4 and 8 with uracil residues. The Cα carbons of repeats 4 and 8 were superimposed and their interaction with Ura-7B and Ura-3B, respectively, are shown. Ura-3B that interacts with repeat 8 is shown in yellow. Ura-7B that interacts with repeat 4 is shown in gray. Hydrogen bonds with Ura-3B are indicated with red dotted lines, and the hydrogen bond between Gln-975 and Ura-7B is shown with a black dotted line. Ura-7B stacks between Arg-1008 and His-972. The position of Asn-971, which does not contact Ura-7B, is shown for reference.(C) Interaction of repeats 4 and 8 with uracil residues is shown as in (B), but only the side chains of Asn-971, Gln-975, and Arg-1008 (Ura-7B) and those of Asn-1122, Gln-1126, and His-1159 (Ura-3B) are shown.(D) Interaction of repeat 3 with Ade-8B. Hydrogen bonds with Gln-939 are indicated with black dotted lines, and the van der Waals contact with Cys-935 is indicated with a green dotted line. Ade-8B stacks between Arg-936 and His-972. The figure was prepared with MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Bacon, 1997).

The above figures are reprinted by permission from Cell Press: Cell (2002, 110, 501-512) copyright 2002.

Figures were selected by the author.