3KJO Dna Binding Protein Dna date Nov 03, 2009
title Crystal Structure Of Hpot1v2-Dtrud(Agggttag)
authors J.Nandakumar, T.R.Cech, E.R.Podell
compound source
Molecule: Protection Of Telomeres Protein 1
Chain: A
Fragment: Unp Residues 1-299
Synonym: Hpot1, Pot1-Like Telomere End-Binding Protein
Engineered: Yes
Other_details: Putative Splice Variant Of Hpot1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pot1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Bacmid
Expression_system_plasmid: Pfastbac

Molecule: Dnarna (5'-D(T)-R(Pu)-D(Papgpgpgptptpap
Chain: B
Engineered: Yes
Other_details: Single-Stranded Dna Containing An Ru Ribonuc Substitution At Position 4.

Synthetic: Yes
Other_details: 10mer Synthetic Oligonucleotide Containing H Telomeric Repeat Sequence With A Single Ribonucleotide At P
symmetry Space Group: C 2 2 21
R_factor 0.228 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
101.867 103.591 71.736 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å

Primary referenceHow telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA., Nandakumar J, Podell ER, Cech TR, Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):651-656. Epub 2009 Dec 22. PMID:20080730
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3kjo.pdb1.gz) 55 Kb
  • CSU: Contacts of Structural Units for 3KJO
  • Structure Factors (440 Kb)
  • Retrieve 3KJO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KJO from S2C, [Save to disk]
  • Re-refined 3kjo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KJO 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 3KJO
  • 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 3KJO, from MSDmotif at EBI
  • Fold representative 3kjo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kjo] [3kjo_B] [3kjo_A]
  • SWISS-PROT database: [Q9NUX5]
  • Domain organization of [POTE1_HUMAN] by SWISSPFAM
  • Domain found in 3KJO: [Telo_bind ] by SMART
  • Other resources with information on 3KJO
  • Community annotation for 3KJO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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