5NL0 Chromatin Binding Protein Dna date Apr 03, 2017
title Crystal Structure Of A 197-Bp Palindromic 601l Nucleosome In With Linker Histone H1
authors I.Garcia-Saez, C.Petosa, S.Dimitrov
compound source
Molecule: Histone H3.2
Chain: A, E, K
Engineered: Yes
Other_details: The Core Histones In The Uploaded Coordinate Those From X. Laevis While Those In The Crystal Are Human. For The Discrepancy Is That The Structure Was Solved Using As A Molecular Replacement Template (Because It Had The Sam Sequence And Therefore Was The Closest High-Res Structure A .;
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F, L
Engineered: Yes
Other_details: The Core Histones In The Uploaded Coordinate Those From X. Laevis While Those In The Crystal Are Human. For The Discrepancy Is That The Structure Was Solved Using As A Molecular Replacement Template (Because It Had The Sam Sequence And Therefore Was The Closest High-Res Structure A .;

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1
Chain: C, G, M
Engineered: Yes
Other_details: The Core Histones In The Uploaded Coordinate Those From X. Laevis While Those In The Crystal Are Human. For The Discrepancy Is That The Structure Was Solved Using As A Molecular Replacement Template (Because It Had The Sam Sequence And Therefore Was The Closest High-Res Structure A .;

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H, N
Synonym: H2b1.1
Engineered: Yes
Other_details: The Core Histones In The Uploaded Coordinate Those From X. Laevis While Those In The Crystal Are Human. For The Discrepancy Is That The Structure Was Solved Using As A Molecular Replacement Template (Because It Had The Sam Sequence And Therefore Was The Closest High-Res Structure A .;

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (197-Mer)
Chain: I, S
Engineered: Yes
Other_details: There Are Only 193 Bp In The Structure Where Are 197 Bp In The Crystal; Putatively This Could Be Because Pairs At The Tip Of Each Linker Are Denatured And Therefore Visible.;

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (197-Mer)
Chain: J, T
Engineered: Yes
Other_details: There Are Only 193 Bp In The Structure Where Are 197 Bp In The Crystal; Putatively This Could Be Because Pairs At The Tip Of Each Linker Are Denatured And Therefore Visible.;

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H1.0-B
Chain: Z
Synonym: H1-Sa,H1d,Histone H1(0)-2,Histone H5a,Xlh5a
Engineered: Yes
Other_details: Only The H1.0b Globular Domain Was Visible I Structure. The Coordinates Of This Chain Are Those Of A Hom Model Built From Chicken Gh5 (Pdb 1hst).

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: H1f0-B
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.240 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.725 405.737 348.162 90.00 90.00 90.00
method X-Ray Diffractionresolution 5.40 Å
Gene
Ontology
ChainFunctionProcessComponent
A, K, E


F, B, L


M, C, G


N, H, D


Z


Primary referenceStructure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1., Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G, Reymer A, Syed SH, Lone IN, Tonchev O, Crucifix C, Menoni H, Papin C, Skoufias DA, Kurumizaka H, Lavery R, Hamiche A, Hayes JJ, Schultz P, Angelov D, Petosa C, Dimitrov S, Mol Cell. 2017 May 4;66(3):384-397.e8. doi: 10.1016/j.molcel.2017.04.012. PMID:28475873
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (955 Kb) [Save to disk]
  • Biological Unit Coordinates (5nl0.pdb1.gz) 637 Kb
  • Biological Unit Coordinates (5nl0.pdb2.gz) 311 Kb
  • CSU: Contacts of Structural Units for 5NL0
  • Structure Factors (603 Kb)
  • Retrieve 5NL0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NL0 from S2C, [Save to disk]
  • Re-refined 5nl0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5NL0 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 5NL0
  • 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 5nl0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5nl0_B] [5nl0_S] [5nl0_M] [5nl0_H] [5nl0_J] [5nl0_I] [5nl0_L] [5nl0_N] [5nl0_E] [5nl0_F] [5nl0_D] [5nl0] [5nl0_C] [5nl0_G] [5nl0_Z] [5nl0_K] [5nl0_T] [5nl0_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NL0
  • Community annotation for 5NL0 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science