4PKD Gene Regulation date May 14, 2014
title U1-70k In Complex With U1 Snrna Stem-Loops 1 And U1-A Rrm In With Stem-Loop 2
authors C.Oubridge, Y.Kondo, A.M.Van Roon, K.Nagai
compound source
Molecule: U1 Snrna Stem-Loops 1 And 2 (55-Mer)
Chain: V
Engineered: Yes
Other_details: Rna Is A Dumbell-Shaped Fusion Of U1 Snrna S And The Apical Part Of U1 Snrna Stem-Loop 2 Joined By A 3 B Linker. Transcribed By T7 Rna Polymerase From A Linearised Template.;
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: See Compound Details.

Molecule: U1 Small Nuclear Ribonucleoprotein A,U1 Small Nuc Ribonucleoprotein 70 Kda;
Chain: B
Synonym: U1a,Snrnp70
Engineered: Yes
Mutation: Yes
Other_details: Both This Protein And U1-70k Are Expressed T A Fusion Protein. The C-Terminus Of U1-A And The Linker Pep Disordered In The Structure. The Two Proteins Have Been Giv Separate Chain Identifiers So That Their Normal Numbering I Preserved., U1-A And This Protein Are Expressed Together As Protein. The C-Terminus Of U1-A And The Linker Peptide Are In The Structure. The Two Proteins Have Been Given Separate Identifiers So That Their Normal Numbering Is Preserved.

Organism_scientific: Sus Scrofa, Homo Sapiens
Organism_common: Pig, Human
Organism_taxid: 9823, 9606
Gene: Snrpa, Snrnp70, Rnpu1z, Rpu1, Snrp70, U1ap1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet13
symmetry Space Group: C 1 2 1
R_factor 0.197 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
80.220 66.600 93.730 90.00 110.95 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand GTP, IMD, MG enzyme

Primary referenceCrystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition., Kondo Y, Oubridge C, van Roon AM, Nagai K, Elife. 2015 Jan 2;4. doi: 10.7554/eLife.04986. PMID:25555158
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (4pkd.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 4PKD
  • CSU: Contacts of Structural Units for 4PKD
  • Structure Factors (907 Kb)
  • Retrieve 4PKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PKD from S2C, [Save to disk]
  • Re-refined 4pkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PKD 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 4PKD
  • 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
  • 3D motif for 4PKD, from MSDmotif at EBI
  • Fold representative 4pkd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pkd] [4pkd_V] [4pkd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4PKD: [RRM ] by SMART
  • Other resources with information on 4PKD
  • Community annotation for 4PKD at PDBWiki (http://pdbwiki.org)

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