4M7A Rna Binding Protein date Aug 12, 2013
title Crystal Structure Of Lsm2-8 Complex Bound To The 3' End Sequ Snrna
authors L.Zhou, J.Hang, Y.Zhou, R.Wan, G.Lu, C.Yan, Y.Shi
compound source
Molecule: U6 Snrna-Associated Sm-Like Protein Lsm8
Chain: A, H
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
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: U6 Snrna-Associated Sm-Like Protein Lsm2
Chain: B, I
Synonym: Small Nuclear Ribonucleoprotein D Homolog Snp3
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae
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, J
Synonym: Smx4 Protein
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae
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 Lsm6
Chain: D, K
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
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 Lsm5
Chain: E, L
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
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 Lsm7
Chain: F, M
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
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 Lsm4
Chain: G, N
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
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
Chain: O, P
Engineered: Yes

Synthetic: Yes
Other_details: The Rna Oligo Is Synthesized By Takara
symmetry Space Group: C 1 2 1
R_factor 0.245 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.624 78.379 140.565 90.00 100.58 90.00
method X-Ray Diffractionresolution 2.78 Å
Gene
Ontology
ChainFunctionProcessComponent
A, H


B, I


E, L


F, M


J, C


K, D


N, G


Primary referenceCrystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA., Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y, Nature. 2013 Nov 17. doi: 10.1038/nature12803. PMID:24240276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (368 Kb) [Save to disk]
  • Biological Unit Coordinates (4m7a.pdb1.gz) 180 Kb
  • Biological Unit Coordinates (4m7a.pdb2.gz) 182 Kb
  • Biological Unit Coordinates (4m7a.pdb3.gz) 358 Kb
  • CSU: Contacts of Structural Units for 4M7A
  • Structure Factors (532 Kb)
  • Retrieve 4M7A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M7A from S2C, [Save to disk]
  • Re-refined 4m7a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4M7A 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 4M7A
  • 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
  • 3D motif for 4M7A, from MSDmotif at EBI
  • Fold representative 4m7a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m7a_B] [4m7a_C] [4m7a_L] [4m7a_I] [4m7a_G] [4m7a_J] [4m7a_P] [4m7a_O] [4m7a_E] [4m7a_H] [4m7a_D] [4m7a_M] [4m7a_A] [4m7a_K] [4m7a] [4m7a_F] [4m7a_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4M7A: [Sm ] by SMART
  • Other resources with information on 4M7A
  • Community annotation for 4M7A at PDBWiki (http://pdbwiki.org)

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