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PDBsum entry 3jcm
Go to PDB code: 
protein dna_rna ligands Protein-protein interface(s) links
Transcription PDB id
3jcm

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
2174 a.a.
429 a.a.
416 a.a.
734 a.a.
279 a.a.
139 a.a.
126 a.a.
843 a.a.
1686 a.a.
79 a.a.
73 a.a.
77 a.a.
90 a.a.
72 a.a.
70 a.a.
70 a.a.
71 a.a.
65 a.a.
92 a.a.
77 a.a.
74 a.a.
77 a.a.
66 a.a.
77 a.a.
DNA/RNA
Ligands
GTP
M7M
PDB id:
3jcm
Name: Transcription
Title: Cryo-em structure of the spliceosomal u4/u6.U5 tri-snrnp
Structure: Pre-mRNA-splicing factor 8. Chain: a. U4/u6 small nuclear ribonucleoprotein prp4. Chain: b. Synonym: pre-mRNA-processing protein 4. Pre-mRNA-processing factor 31. Chain: i. Pre-mRNA-splicing factor 6. Chain: g.
Source: Saccharomyces cerevisiae s288c. Organism_taxid: 559292. Strain: s288c. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Strain: s288c
Authors: R.Wan,C.Yan,R.Bai,L.Wang,M.Huang,C.C.Wong,Y.Shi
Key ref: R.Wan et al. (2016). The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis. Science, 351, 466-475. PubMed id: 26743623 DOI: 10.1126/science.aad6466
Date:
23-Dec-15     Release date:   24-Feb-16    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P33334  (PRP8_YEAST) -  Pre-mRNA-splicing factor 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2413 a.a.
2174 a.a.
Protein chain
Pfam   ArchSchema ?
P20053  (PRP4_YEAST) -  U4/U6 small nuclear ribonucleoprotein PRP4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		465 a.a.
429 a.a.
Protein chain
Pfam   ArchSchema ?
P49704  (PRP31_YEAST) -  Pre-mRNA-processing factor 31 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		494 a.a.
416 a.a.
Protein chain
Pfam   ArchSchema ?
P19735  (PRP6_YEAST) -  Pre-mRNA-splicing factor 6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		899 a.a.
734 a.a.
Protein chain
Pfam   ArchSchema ?
Q03338  (PRP3_YEAST) -  U4/U6 small nuclear ribonucleoprotein PRP3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		469 a.a.
279 a.a.
Protein chain
Pfam   ArchSchema ?
Q06819  (DIB1_YEAST) -  Spliceosomal protein DIB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		143 a.a.
139 a.a.
Protein chain
Pfam   ArchSchema ?
P39990  (SNU13_YEAST) -  13 kDa ribonucleoprotein-associated protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		126 a.a.
126 a.a.
Protein chain
Pfam   ArchSchema ?
P36048  (SN114_YEAST) -  Pre-mRNA-splicing factor SNU114 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		1008 a.a.
843 a.a.
Protein chain
Pfam   ArchSchema ?
P32639  (BRR2_YEAST) -  Pre-mRNA-splicing helicase BRR2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2163 a.a.
1686 a.a.
Protein chains
Pfam   ArchSchema ?
P43321  (SMD3_YEAST) -  Small nuclear ribonucleoprotein Sm D3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		101 a.a.
79 a.a.
Protein chains
Pfam   ArchSchema ?
P40018  (RSMB_YEAST) -  Small nuclear ribonucleoprotein-associated protein B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		196 a.a.
73 a.a.
Protein chains
Pfam   ArchSchema ?
Q02260  (SMD1_YEAST) -  Small nuclear ribonucleoprotein Sm D1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		146 a.a.
77 a.a.
Protein chains
Pfam   ArchSchema ?
Q06217  (SMD2_YEAST) -  Small nuclear ribonucleoprotein Sm D2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		110 a.a.
90 a.a.
Protein chains
Pfam   ArchSchema ?
Q12330  (RUXE_YEAST) -  Small nuclear ribonucleoprotein E from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		94 a.a.
72 a.a.
Protein chains
Pfam   ArchSchema ?
P54999  (RUXF_YEAST) -  Small nuclear ribonucleoprotein F from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		86 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P40204  (RUXG_YEAST) -  Small nuclear ribonucleoprotein G from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		77 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P40204  (RUXG_YEAST) -  Small nuclear ribonucleoprotein G from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		77 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
P47093  (LSM8_YEAST) -  U6 snRNA-associated Sm-like protein LSm8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		109 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38203  (LSM2_YEAST) -  U6 snRNA-associated Sm-like protein LSm2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		95 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
P57743  (LSM3_YEAST) -  U6 snRNA-associated Sm-like protein LSm3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		89 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
Q06406  (LSM6_YEAST) -  U6 snRNA-associated Sm-like protein LSm6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		86 a.a.
74 a.a.
Protein chain
Pfam   ArchSchema ?
P40089  (LSM5_YEAST) -  U6 snRNA-associated Sm-like protein LSm5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		93 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P53905  (LSM7_YEAST) -  U6 snRNA-associated Sm-like protein LSm7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		115 a.a.
66 a.a.
Protein chain
Pfam   ArchSchema ?
P40070  (LSM4_YEAST) -  U6 snRNA-associated Sm-like protein LSm4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		187 a.a.
77 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-A-A-A-A-A-U-U-A-A-G-G-U-A-U-G-U-A-U-U 20 bases
  A-A-U-A-C-A-G-A-G-A-U-C-A-G-C-A-G-U-U-C-C-C-C-U-G-C-A-U-A-A-G-G-A-U-G-A-A-C-C- 45 bases
  A-U-C-C-U-U-A-U-G-C-A-C-G-G-G-A-A-A-U-A-C-G-C-A-U-A-U-C-A-G-U-G-A-G-G-A-U-U-C- 85 bases
  G-G-A-G-G-U-C-A-A-C-A-U-C-A-A-G-A-A-C-U-G-U-G-G-G-C-G-C-C-U-A-U-A-G-A-A-C-U-U- 113 bases

 Enzyme reactions 
   Enzyme class: Chain N: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 = ADP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1126/science.aad6466 Science 351:466-475 (2016)
PubMed id: 26743623  
 
 
The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.
R.Wan, C.Yan, R.Bai, L.Wang, M.Huang, C.C.Wong, Y.Shi.
 
  ABSTRACT  
 
Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (snRNP), the U4 and U6 small nuclear RNA (snRNA) duplex, and a number of protein factors. Here we report the three-dimensional structure of a Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at an overall resolution of 3.8 angstroms by single-particle electron cryomicroscopy. The local resolution for the core regions of the tri-snRNP reaches 3.0 to 3.5 angstroms, allowing construction of a refined atomic model. Our structure contains U5 snRNA, the extensively base-paired U4/U6 snRNA, and 30 proteins including Prp8 and Snu114, which amount to 8495 amino acids and 263 nucleotides with a combined molecular mass of ~1 megadalton. The catalytic nucleotide U80 from U6 snRNA exists in an inactive conformation, stabilized by its base-pairing interactions with U4 snRNA and protected by Prp3. Pre-messenger RNA is bound in the tri-snRNP through base-pairing interactions with U6 snRNA and loop I of U5 snRNA. This structure, together with that of the spliceosome, reveals the molecular choreography of the snRNAs in the activation process of the spliceosomal ribozyme.
 

 

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