4M7D Rna Binding Protein date Aug 12, 2013
title Crystal Structure Of Lsm2-8 Complex Bound To The Rna Fragmen
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: Rna Oligo Is Synthesized By Takara
symmetry Space Group: C 1 2 1
R_factor 0.240 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.539 78.483 142.987 90.00 103.17 90.00
method X-Ray Diffractionresolution 2.60 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] (374 Kb) [Save to disk]
  • Biological Unit Coordinates (4m7d.pdb1.gz) 186 Kb
  • Biological Unit Coordinates (4m7d.pdb2.gz) 181 Kb
  • CSU: Contacts of Structural Units for 4M7D
  • Structure Factors (694 Kb)
  • Retrieve 4M7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M7D from S2C, [Save to disk]
  • Re-refined 4m7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4M7D 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 4M7D
  • 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 4M7D, from MSDmotif at EBI
  • Fold representative 4m7d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m7d_K] [4m7d_J] [4m7d_O] [4m7d_F] [4m7d] [4m7d_A] [4m7d_G] [4m7d_H] [4m7d_E] [4m7d_L] [4m7d_B] [4m7d_M] [4m7d_P] [4m7d_D] [4m7d_I] [4m7d_C] [4m7d_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4M7D: [Sm ] by SMART
  • Other resources with information on 4M7D
  • Community annotation for 4M7D at PDBWiki (http://pdbwiki.org)

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