5VSU Splicing date May 12, 2017
title Structure Of Yeast U6 Snrnp With 2'-Phosphate Terminated U6
authors E.J.Montemayor
compound source
Molecule: U4u6 Snrna-Associated-Splicing Factor Prp24
Chain: A
Synonym: U4u6 Snrnp Protein
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Prp24, Ymr268c, Ym8156.10c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm2
Chain: B
Synonym: Small Nuclear Ribonucleoprotein D Homolog Snp3
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm2, Smx5, Snp3, Ybl026w, Ybl0425
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm3
Chain: C
Synonym: Smx4 Protein
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm3, Smx4, Uss2, Ylr438c-A
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm4
Chain: D
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm4, Sdb23, Uss1, Yer112w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm5
Chain: E
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm5, Yer146w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm6
Chain: F
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm6, Ydr378c, D9481.18
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm7
Chain: G
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm7, Ynl147w, N1202, N1780
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm8
Chain: H
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Lsm8, Yjr022w, J1464, Yjr83.16
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Saccharomyces Cerevisiae Strain T8 Chromosome Xii
Chain: I
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.157 114.728 179.844 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


Primary referenceArchitecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA., Montemayor EJ, Didychuk AL, Yake AD, Sidhu GK, Brow DA, Butcher SE, Nat Commun. 2018 May 1;9(1):1749. doi: 10.1038/s41467-018-04145-4. PMID:29717126
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (197 Kb) [Save to disk]
  • Biological Unit Coordinates (5vsu.pdb1.gz) 189 Kb
  • CSU: Contacts of Structural Units for 5VSU
  • Structure Factors (370 Kb)
  • Retrieve 5VSU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VSU from S2C, [Save to disk]
  • View 5VSU 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 5VSU
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5vsu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vsu_A] [5vsu_H] [5vsu_D] [5vsu_F] [5vsu_I] [5vsu_G] [5vsu_C] [5vsu_E] [5vsu_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VSU
  • Community annotation for 5VSU at PDBWiki (http://pdbwiki.org)

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