Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - ABCDEFGHI Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer -A7BC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 360484.72 
• Atom Count: 19123 
• Residue Count: 2780 
• Unique protein chains: 10
• Unique nucleic acid chains: 2

5GAM

Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

• DOI: 10.2210/pdb5GAM/pdb
• EMDataBank: EMD-8011

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae


• Deposited: 2015-12-15 Released: 2016-02-03 
• Deposition Author(s): Nguyen, T.H.D., Galej, W.P., Bai, X.C., Oubridge, C., Scheres, S.H.W., Newman, A.J., Nagai, K.
• Funding Organization(s): Medical Research Council (United Kingdom) 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Angstrom resolution

Nguyen, T.H.D., Galej, W.P., Bai, X.C., Oubridge, C., Scheres, S.H.W., Newman, A.J., Nagai, K.

(2016) Nature 530: 298-302

• PubMed: 26829225 
• DOI: 10.1038/nature16940
• Primary Citation of Related Structures:  
  5GAN, 5GAP, 5GAO
• Also Cited By: 5MQ0, 5MPS


• PubMed Abstract: 
  

U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.

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Related Citations: 

• The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
  Nguyen, T.H.D.,Galej, W.,Bai, X.C.,Savva, C.G.,Newman, A.J.,Scheres, S.H.W.,Nagai, K.
  (2015) Nature 523: 47




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Organizational Affiliation: 

MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing factor 8	A	735	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P33334

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing factor SNU114	C	1008	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P36048

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein-associated protein B	b	196	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40018

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein E	e	94	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q12330

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein F	f	86	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P54999

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein G	g	77	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40204

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
Unknown polypeptide	x	18	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein Sm D3	d	101	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P43321

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein Sm D1	h	146	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02260

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein Sm D2	j	110	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q06217

Entity ID: 1
Molecule	Chains	Length	Organism
U5 snRNA	U	178	Saccharomyces cerevisiae

Entity ID: 4
Molecule	Chains	Length	Organism
U6 snRNA, 5' end	W	31	Saccharomyces cerevisiae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GTP	C	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	x	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-12-15 
• Released Date: 2016-02-03 
• Deposition Author(s): Nguyen, T.H.D., Galej, W.P., Bai, X.C., Oubridge, C., Scheres, S.H.W., Newman, A.J., Nagai, K.

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Funding Organization	Country	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History 

• Version 1.0: 2016-02-03
  Type: Initial release
• Version 1.1: 2017-08-30
  Type: Author supporting evidence, Data collection, Derived calculations