PDBsum entry: 3cw1

Splicing

PDB id: 3cw1

Contents

Protein chains

76 a.a.* *

64 a.a.* *

77 a.a.* *

88 a.a.* *

76 a.a.* *

75 a.a.* *

73 a.a.* *

120 a.a.* *

57 a.a.* *

70 a.a.* *

89 a.a.* *

54 a.a.* *

DNA/RNA

Metals

_ZN ×4

* Residue conservation analysis

* C-alpha coords only

PDB id:

3cw1

Name:

Splicing

Title:

Crystal structure of human spliceosomal u1 snrnp

Structure:

U1 snrna. Chain: v, v, w, x. Fragment: nucleotides 57-82 absent, replaced with kissing l engineered: yes. Mutation: yes. Small nuclear ribonucleoprotein sm d3. Chain: d, s, t, u. Synonym: snrnp core protein d3, sm-d3. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rnu1a. Other_details: in vitro transcribed with t7 RNA polymerase. Gene: snrpd3. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: coexpressed with sm b, entity 2.

Resolution:

5.49Å R-factor: not given

Authors:

D.A.Pomeranz Krummel,C.Oubridge,A.K.Leung,J.Li,K.Nagai

Key ref:

D.A.Pomeranz Krummel et al. (2009). Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature, 458, 475-480. PubMed id: 19325628 DOI: 10.1038/nature07851

Date:

21-Apr-08 Release date: 24-Mar-09

Protein chains

P62318  (SMD3_HUMAN) -  Small nuclear ribonucleoprotein Sm D3

Seq: 126 a.a.

Struc: 76 a.a.*

Protein chains

P14678  (RSMB_HUMAN) -  Small nuclear ribonucleoprotein-associated proteins B and B'

Seq: 240 a.a.

Struc: 64 a.a.

Protein chains

P62314  (SMD1_HUMAN) -  Small nuclear ribonucleoprotein Sm D1

Seq: 119 a.a.

Struc: 77 a.a.

Protein chains

P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2

Seq: 118 a.a.

Struc: 88 a.a.

Protein chains

P62306  (RUXF_HUMAN) -  Small nuclear ribonucleoprotein F

Seq: 86 a.a.

Struc: 76 a.a.

Protein chains

P62304  (RUXE_HUMAN) -  Small nuclear ribonucleoprotein E

Seq: 92 a.a.

Struc: 75 a.a.

Protein chains

P62308  (RUXG_HUMAN) -  Small nuclear ribonucleoprotein G

Seq: 76 a.a.

Struc: 73 a.a.

Protein chains

P08621  (RU17_HUMAN) -  U1 small nuclear ribonucleoprotein 70 kDa

Seq: 437 a.a.

Struc: 120 a.a.

Protein chains

P09234  (RU1C_HUMAN) -  U1 small nuclear ribonucleoprotein C

Seq: 159 a.a.

Struc: 57 a.a.*

Protein chain

P62306  (RUXF_HUMAN) -  Small nuclear ribonucleoprotein F

Seq: 86 a.a.

Struc: 70 a.a.

Protein chains

P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2

Seq: 118 a.a.

Struc: 89 a.a.

Protein chain

P09234  (RU1C_HUMAN) -  U1 small nuclear ribonucleoprotein C

Seq: 159 a.a.

Struc: 54 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: catalytic step 2 spliceosome (10 terms)
• Biological process: gene expression (12 terms)
• Biochemical function: histone pre-mRNA DCP binding (7 terms)

reference

DOI no: 10.1038/nature07851

Nature 458:475-480 (2009)

PubMed id: 19325628

Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.

D.A.Pomeranz Krummel, C.Oubridge, A.K.Leung, J.Li, K.Nagai.

ABSTRACT

Human spliceosomal U1 small nuclear ribonucleoprotein particles (snRNPs), which consist of U1 small nuclear RNA and ten proteins, recognize the 5' splice site within precursor messenger RNAs and initiate the assembly of the spliceosome for intron excision. An electron density map of the functional core of U1 snRNP at 5.5 A resolution has enabled us to build the RNA and, in conjunction with site-specific labelling of individual proteins, to place the seven Sm proteins, U1-C and U1-70K into the map. Here we present the detailed structure of a spliceosomal snRNP, revealing a hierarchical network of intricate interactions between subunits. A striking feature is the amino (N)-terminal polypeptide of U1-70K, which extends over a distance of 180 A from its RNA binding domain, wraps around the core domain consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition. The structure of U1 snRNP provides insights into U1 snRNP assembly and suggests a possible mechanism of 5'-splice-site recognition.

Selected figure(s)

Figure 2.
Figure 2: Structure of the U1 snRNP core domain. a, The Sm proteins and the experimental electron density map (contoured at 1 ). Cartwheel-shaped density in the central hole of the U1 snRNP core domain is attributed to the seven Sm site nucleotides. b, The N terminus of Sm-D2 supporting helix H. The extended polypeptide of U1-70K interacts with Sm-D2. SeMet anomalous peaks from natural (Met 67; red) and engineered Met residues (I41M, E49M and E61M; orange) of U1-70K and of Sm-D2 (Met 11; cyan). The asterisk indicates a 'bump' due to Phe 24 of Sm-D2. c, The N terminus of Sm-B interacting with the phosphate backbone of SL2. Navy blue spheres, anomalous peaks from SeMet-labelled Sm-B.

Figure 5.
Figure 5: Model of the complete human U1 snRNP. a, Overview of a model of the complete U1 snRNP. Truncated SL2 was extended with A-form RNA and the crystal structure of the U1A–RNA complex^19 was appended to the extended helix. The internal loop of SL2, consisting of four consecutive non-Watson–Crick base pairs (red), is in a position to interact with Sm-B and Sm-D1. b, Two views of the complete U1 snRNP model approximately 45° apart, with surface representation superimposed. Closely matching images are found in the gallery of negatively stained images of U1 snRNP reported previously^23, ^24.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2009, 458, 475-480) copyright 2009.

Figures were selected by the author.