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PDBsum entry 3cw1

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protein dna_rna metals links
Splicing PDB id
3cw1
Jmol
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    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P62318  (SMD3_HUMAN) -  Small nuclear ribonucleoprotein Sm D3
Seq:
Struc:
126 a.a.
76 a.a.*
Protein chains
Pfam   ArchSchema ?
P14678  (RSMB_HUMAN) -  Small nuclear ribonucleoprotein-associated proteins B and B'
Seq:
Struc:
240 a.a.
64 a.a.
Protein chains
Pfam   ArchSchema ?
P62314  (SMD1_HUMAN) -  Small nuclear ribonucleoprotein Sm D1
Seq:
Struc:
119 a.a.
77 a.a.
Protein chains
Pfam   ArchSchema ?
P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2
Seq:
Struc:
118 a.a.
88 a.a.
Protein chains
Pfam   ArchSchema ?
P62306  (RUXF_HUMAN) -  Small nuclear ribonucleoprotein F
Seq:
Struc:
86 a.a.
76 a.a.
Protein chains
Pfam   ArchSchema ?
P62304  (RUXE_HUMAN) -  Small nuclear ribonucleoprotein E
Seq:
Struc:
92 a.a.
75 a.a.
Protein chains
Pfam   ArchSchema ?
P62308  (RUXG_HUMAN) -  Small nuclear ribonucleoprotein G
Seq:
Struc:
76 a.a.
73 a.a.
Protein chains
Pfam   ArchSchema ?
P08621  (RU17_HUMAN) -  U1 small nuclear ribonucleoprotein 70 kDa
Seq:
Struc:
437 a.a.
120 a.a.
Protein chains
Pfam   ArchSchema ?
P09234  (RU1C_HUMAN) -  U1 small nuclear ribonucleoprotein C
Seq:
Struc:
159 a.a.
57 a.a.*
Protein chain
Pfam   ArchSchema ?
P62306  (RUXF_HUMAN) -  Small nuclear ribonucleoprotein F
Seq:
Struc:
86 a.a.
70 a.a.
Protein chains
Pfam   ArchSchema ?
P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2
Seq:
Struc:
118 a.a.
89 a.a.
Protein chain
Pfam   ArchSchema ?
P09234  (RU1C_HUMAN) -  U1 small nuclear ribonucleoprotein C
Seq:
Struc:
159 a.a.
54 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     catalytic step 2 spliceosome   17 terms 
  Biological process     gene expression   14 terms 
  Biochemical function     nucleic acid binding     8 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 an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21516107 A.K.Leung, K.Nagai, and J.Li (2011).
Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.
  Nature, 473, 536-539.
PDB codes: 2y9a 2y9b 2y9c 2y9d
21522132 B.Pradet-Balade, C.Girard, S.Boulon, C.Paul, K.Azzag, R.Bordonné, E.Bertrand, and C.Verheggen (2011).
CRM1 controls the composition of nucleoplasmic pre-snoRNA complexes to licence them for nucleolar transport.
  EMBO J, 30, 2205-2218.  
21362553 S.Sharma, C.Maris, F.H.Allain, and D.L.Black (2011).
U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression.
  Mol Cell, 41, 579-588.  
20727772 A.Chari, and U.Fischer (2010).
Cellular strategies for the assembly of molecular machines.
  Trends Biochem Sci, 35, 676-683.  
20554048 A.R.Ferré-D'Amaré (2010).
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
  Methods, 52, 159-167.  
20010808 C.J.David, M.Chen, M.Assanah, P.Canoll, and J.L.Manley (2010).
HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer.
  Nature, 463, 364-368.  
20421206 E.Kühn-Hölsken, C.Lenz, A.Dickmanns, H.H.Hsiao, F.M.Richter, B.Kastner, R.Ficner, and H.Urlaub (2010).
Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry.
  Nucleic Acids Res, 38, 5581-5593.  
21113136 G.Weber, S.Trowitzsch, B.Kastner, R.Lührmann, and M.C.Wahl (2010).
Functional organization of the Sm core in the crystal structure of human U1 snRNP.
  EMBO J, 29, 4172-4184.
PDB code: 3pgw
20194618 K.Ohe, and A.Mayeda (2010).
HMGA1a trapping of U1 snRNP at an authentic 5' splice site induces aberrant exon skipping in sporadic Alzheimer's disease.
  Mol Cell Biol, 30, 2220-2228.  
20801768 M.Bragulat, M.Meyer, S.Macías, M.Camats, M.Labrador, and J.Vilardell (2010).
RPL30 regulation of splicing reveals distinct roles for Cbp80 in U1 and U2 snRNP cotranscriptional recruitment.
  RNA, 16, 2033-2041.  
20616058 M.D.Daugherty, D.S.Booth, B.Jayaraman, Y.Cheng, and A.D.Frankel (2010).
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.
  Proc Natl Acad Sci U S A, 107, 12481-12486.  
20112371 M.Lech, V.Skuginna, O.P.Kulkarni, J.Gong, T.Wei, R.W.Stark, C.Garlanda, A.Mantovani, and H.J.Anders (2010).
Lack of SIGIRR/TIR8 aggravates hydrocarbon oil-induced lupus nephritis.
  J Pathol, 220, 596-607.  
21172658 M.M.Golas, B.Sander, S.Bessonov, M.Grote, E.Wolf, B.Kastner, H.Stark, and R.Lührmann (2010).
3D cryo-EM structure of an active step I spliceosome and localization of its catalytic core.
  Mol Cell, 40, 927-938.  
20071748 M.R.Alexander, A.K.Wheatley, R.J.Center, and D.F.Purcell (2010).
Efficient transcription through an intron requires the binding of an Sm-type U1 snRNP with intact stem loop II to the splice donor.
  Nucleic Acids Res, 38, 3041-3053.  
20106955 M.W.Górna, Z.Pietras, Y.C.Tsai, A.J.Callaghan, H.Hernández, C.V.Robinson, and B.F.Luisi (2010).
The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome.
  RNA, 16, 553-562.  
20627589 M.Zhou, and C.V.Robinson (2010).
When proteomics meets structural biology.
  Trends Biochem Sci, 35, 522-529.  
20192997 N.H.Kattah, M.G.Kattah, and P.J.Utz (2010).
The U1-snRNP complex: structural properties relating to autoimmune pathogenesis in rheumatic diseases.
  Immunol Rev, 233, 126-145.  
21080498 S.Valadkhan, and Y.Jaladat (2010).
The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine.
  Proteomics, 10, 4128-4141.  
19424134 A.Bhattacharya (2009).
Protein structures: Structures of desire.
  Nature, 459, 24-27.  
19325619 C.C.Query (2009).
Structural biology: Spliceosome subunit revealed.
  Nature, 458, 418-419.  
19604473 C.Oubridge, D.A.Krummel, A.K.Leung, J.Li, and K.Nagai (2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
  Structure, 17, 930-938.  
19784376 H.Hernández, O.V.Makarova, E.M.Makarov, N.Morgner, Y.Muto, D.P.Krummel, and C.V.Robinson (2009).
Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.
  PLoS One, 4, e7202.  
19373252 J.F.Kugel, and J.A.Goodrich (2009).
In new company: U1 snRNA associates with TAF15.
  EMBO Rep, 10, 454-456.  
19451230 R.Hage, L.Tung, H.Du, L.Stands, M.Rosbash, and T.H.Chang (2009).
A targeted bypass screen identifies Ynl187p, Prp42p, Snu71p, and Cbp80p for stable U1 snRNP/Pre-mRNA interaction.
  Mol Cell Biol, 29, 3941-3952.  
19889981 T.M.Link, P.Valentin-Hansen, and R.G.Brennan (2009).
Structure of Escherichia coli Hfq bound to polyriboadenylate RNA.
  Proc Natl Acad Sci U S A, 106, 19292-19297.
PDB code: 3gib
20514218 Y.Nie, C.Viola, C.Bieniossek, S.Trowitzsch, L.S.Vijay-Achandran, M.Chaillet, F.Garzoni, and I.Berger (2009).
Getting a grip on complexes.
  Curr Genomics, 10, 558-572.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.