4Y0F Dna Binding Protein Dna date Feb 06, 2015
title Crystal Structure Of Human Tdp-43 Rrm1 Domain In Complex Wit Unmodified Single-Stranded Dna
authors C.H.Chiang, P.H.Kuo, L.G.Doudeva, Y.T.Wang, H.S.Yuan
compound source
Molecule: Tar Dna-Binding Protein 43
Chain: A, B
Fragment: Unp Residues 101-191
Synonym: Tdp-43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tardbp, Tdp43
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe30

Molecule: Dna (5'-D(Gptptpgpapgpcpgptpt)-3')
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 65 2 2
R_factor 0.240 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.027 100.027 98.144 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.65 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation., Chiang CH, Grauffel C, Wu LS, Kuo PH, Doudeva LG, Lim C, Shen CK, Yuan HS, Sci Rep. 2016 Feb 17;6:21581. doi: 10.1038/srep21581. PMID:26883171
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (4y0f.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (4y0f.pdb2.gz) 28 Kb
  • CSU: Contacts of Structural Units for 4Y0F
  • Structure Factors (139 Kb)
  • Retrieve 4Y0F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Y0F from S2C, [Save to disk]
  • Re-refined 4y0f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Y0F 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 4Y0F
  • 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 4y0f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4y0f_A] [4y0f_B] [4y0f_C] [4y0f] [4y0f_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4Y0F: [RRM ] by SMART
  • Other resources with information on 4Y0F
  • Community annotation for 4Y0F at PDBWiki (http://pdbwiki.org)

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