5YUF Oncoprotein date Nov 22, 2017
title Crystal Structure Of Pml Ring Tetramer
authors P.Wang, S.Benhend, H.Wu, V.Breitenbach, T.Zhen, F.Jollivet, L.Pere S.Chen, Z.Chen, H.De The, G.Meng
compound source
Molecule: Protein Pml
Chain: A, B, C, D
Synonym: Promyelocytic Leukemia Protein,Ring Finger Protein Tripartite Motif-Containing Protein 19;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pml, Myl, Pp8675, Rnf71, Trim19
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.203 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.510 84.690 86.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
Primary referenceRING tetramerization is required for nuclear body biogenesis and PML sumoylation., Wang P, Benhenda S, Wu H, Lallemand-Breitenbach V, Zhen T, Jollivet F, Peres L, Li Y, Chen SJ, Chen Z, de The H, Meng G, Nat Commun. 2018 Mar 29;9(1):1277. doi: 10.1038/s41467-018-03498-0. PMID:29599493
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (5yuf.pdb1.gz) 91 Kb
  • CSU: Contacts of Structural Units for 5YUF
  • Structure Factors (1880 Kb)
  • Retrieve 5YUF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YUF from S2C, [Save to disk]
  • View 5YUF 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 5YUF
  • 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 5yuf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yuf_D] [5yuf_C] [5yuf_B] [5yuf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YUF
  • Community annotation for 5YUF at PDBWiki (http://pdbwiki.org)

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