5IFE Splicing date Feb 25, 2016
title Crystal Structure Of The Human Sf3b Core Complex
authors C.Cretu, O.Dybkov, E.De Laurentiis, C.L.Will, R.Luhrmann, V.Pena
compound source
Molecule: Splicing Factor 3b Subunit 5
Chain: B
Synonym: Sf3b5,Pre-Mrna-Splicing Factor Sf3b 10 Kda Subunit
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sf3b5, Sf3b10
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Splicing Factor 3b Subunit 1
Chain: C
Synonym: Pre-Mrna-Splicing Factor Sf3b 155 Kda Subunit,Sf3b Spliceosome-Associated Protein 155,Sap 155;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sf3b1, Sap155
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Phd Finger-Like Domain-Containing Protein 5a
Chain: D
Synonym: Phd Finger-Like Domain Protein 5a,Splicing Factor Associated 14 Kda Protein,Sf3b14b;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Phf5a
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Splicing Factor 3b Subunit 3
Chain: A
Synonym: Pre-Mrna-Splicing Factor Sf3b 130 Kda Subunit,Sf3b Staf130,Spliceosome-Associated Protein 130,Sap 130;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sf3b3, Kiaa0017, Sap130
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 21 21 21
R_factor 0.231 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.055 154.436 210.418 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand K, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • protein binding

  • catalytic step 2 spliceosome...
  • B


    C
  • splicing factor binding

  • catalytic step 2 spliceosome...
  • D


    Primary referenceMolecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations., Cretu C, Schmitzova J, Ponce-Salvatierra A, Dybkov O, De Laurentiis EI, Sharma K, Will CL, Urlaub H, Luhrmann R, Pena V, Mol Cell. 2016 Oct 20;64(2):307-319. doi: 10.1016/j.molcel.2016.08.036. Epub 2016, Oct 6. PMID:27720643
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (5ife.pdb1.gz) 350 Kb
  • LPC: Ligand-Protein Contacts for 5IFE
  • CSU: Contacts of Structural Units for 5IFE
  • Structure Factors (4045 Kb)
  • Retrieve 5IFE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IFE from S2C, [Save to disk]
  • Re-refined 5ife structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IFE 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 5IFE
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ife from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ife_B] [5ife_A] [5ife_D] [5ife] [5ife_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5IFE
  • Community annotation for 5IFE at PDBWiki (http://pdbwiki.org)

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