5GAO Transcription date Dec 15, 2015
title Head Region Of The Yeast Spliceosomal U4u6.U5 Tri-Snrnp
authors T.H.D.Nguyen, W.P.Galej, X.C.Bai, C.Oubridge, S.H.W.Scheres, A.J. K.Nagai
compound source
Molecule: Small Nuclear Ribonucleoprotein-Associated Protei
Chain: k
Synonym: Snrnp-B,Sm Protein B,Smb
Other_details: The Smb Protein From The U4 Snrnp Sm Protein C-Terminus Is Disordered In This And Other Previously Repor Structures.;
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: l
Synonym: Sm-D1,Snrnp Core Protein D1
Other_details: The Smd1 Protein From The U4 Snrnp Sm Protei
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: m
Synonym: Sm-D2,Snrnp Core Protein D2
Other_details: The Smd2 Protein From The U4 Snrnp Sm Protei
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: n
Synonym: Sm-D3,Snrnp Core Protein D3, U4 Smd3
Other_details: The Smd3 Protein From The U4 Snrnp Sm Protei
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Small Nuclear Ribonucleoprotein E
Chain: p
Synonym: Snrnp-E,Sm Protein E,Sme
Other_details: The Sme Protein From The U4 Snrnp Sm Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Small Nuclear Ribonucleoprotein F
Chain: q
Synonym: Snrnp-F,Sm Protein F, U4 Smf
Other_details: The Smf Protein From The U4 Snrnp Sm Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Small Nuclear Ribonucleoprotein G
Chain: r
Synonym: Snrnp-G,Sm Protein G, U4 Smg
Other_details: The Smg Protein From The U4 Snrnp Sm Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Snu66
Chain: E
Other_details: Nb: Snu66 Protein Has Been Mostly Fitted As Into Helices And Extended Polypeptide Within The Em Map. Th Do Not Believe The Numbering To Be Accurate And It Is Likel Incorrect.;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Pre-Mrna-Splicing Helicase Brr2
Chain: B
Synonym: Protein Snu246, Brr2 Rna Helicase
Ec: 3.6.4.13
Other_details: Brr2 Rna Helicase Loaded Onto U4 Snrna Stran U4u6 Duplex Between Stem 1 Duplex And The 3' Stem Loop.;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Saccharomyces Cerevisiae Strain Uoa_m2 Chromosome Sequence;
Chain: V
Other_details: This U4 Snrna Region Has A Disordered Region Stem 1 Of The U4u6 Snrna Duplex And Where The Rna Is Loade Brr2 Protein. The Apical Part Of The 3' Stem Loop And The R Following The Sm Site Are Also Disordered.;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123

Molecule: Pre-Mrna-Splicing Factor 8
Chain: A
Synonym: Prp8 Jab1mpn Domain
Other_details: Prp8 Jab1mpn Domain Is Connected To The Res Prp8 Protein By A Flexible Linker Peptide.
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bcy123
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.60 Å
ligand
enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


E


k


l


m


n


p


q


r


Primary referenceCryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution., Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K, Nature. 2016 Feb 18;530(7590):298-302. doi: 10.1038/nature16940. Epub 2016 Feb 1. PMID:26829225
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (475 Kb) [Save to disk]
  • Biological Unit Coordinates (5gao.pdb1.gz) 465 Kb
  • CSU: Contacts of Structural Units for 5GAO
  • Retrieve 5GAO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GAO from S2C, [Save to disk]
    • View 5GAO in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5GAO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gao_A] [5gao_l] [5gao_m] [5gao_B] [5gao_V] [5gao_n] [5gao_p] [5gao_r] [5gao] [5gao_k] [5gao_E] [5gao_q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5GAO: [AAA] [DEXDc] [HELICc] [JAB_MPN] [Sec63] [Sm ] by SMART
    • Other resources with information on 5GAO
  • Community annotation for 5GAO at PDBWiki (http://pdbwiki.org)

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