PDBsum entry 2fj7

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protein dna_rna Protein-protein interface(s) links
Structural protein/DNA PDB id
Protein chains
98 a.a. *
79 a.a. *
107 a.a. *
93 a.a. *
84 a.a. *
* Residue conservation analysis
PDB id:
Name: Structural protein/DNA
Title: Crystal structure of nucleosome core particle containing a poly (da.Dt) sequence element
Structure: 147 bp DNA containing 16 bp poly da element. Chain: i. Engineered: yes. 147 bp DNA containing 16 bp poly dt element. Chain: j. Engineered: yes. Histone h3. Chain: a, e. Engineered: yes.
Source: Synthetic: yes. Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Decamer (from PQS)
3.20Å     R-factor:   0.280     R-free:   0.350
Authors: Y.Bao,C.L.White,K.Luger
Key ref:
Y.Bao et al. (2006). Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure. J Mol Biol, 361, 617-624. PubMed id: 16860337 DOI: 10.1016/j.jmb.2006.06.051
31-Dec-05     Release date:   26-Sep-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P84233  (H32_XENLA) -  Histone H3.2
136 a.a.
98 a.a.*
Protein chain
Pfam   ArchSchema ?
P62799  (H4_XENLA) -  Histone H4
103 a.a.
79 a.a.
Protein chains
Pfam   ArchSchema ?
P06897  (H2A1_XENLA) -  Histone H2A type 1
130 a.a.
107 a.a.*
Protein chains
Pfam   ArchSchema ?
P02281  (H2B11_XENLA) -  Histone H2B 1.1
126 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P62799  (H4_XENLA) -  Histone H4
103 a.a.
84 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   4 terms 
  Biological process     nucleosome assembly   1 term 
  Biochemical function     protein binding     3 terms  


DOI no: 10.1016/j.jmb.2006.06.051 J Mol Biol 361:617-624 (2006)
PubMed id: 16860337  
Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure.
Y.Bao, C.L.White, K.Luger.
Poly(dA.dT) DNA sequence elements are thought to promote transcription by either excluding nucleosomes or by altering their structural or dynamic properties. Here, the stability and structure of a defined nucleosome core particle containing a 16 base-pair poly(dA.dT) element (A16 NCP) was investigated. The A16 NCP requires a significantly higher temperature for histone octamer sliding in vitro compared to comparable nucleosomes that do not contain a poly(dA.dT) element. Fluorescence resonance energy transfer showed that the interactions between the nucleosomal DNA ends and the histone octamer were destabilized in A16 NCP. The crystal structure of A16 NCP was determined to a resolution of 3.2 A. The overall structure was maintained except for local deviations in DNA conformation. These results are consistent with previous in vivo and in vitro observations that poly(dA.dT) elements cause only modest changes in DNA accessibility and modest increases in steady-state transcription levels.
  Selected figure(s)  
Figure 2.
Figure 2. The A[16] element attains a defined position in the crystal lattice. (a) Schematic representation of a nucleosome crystal lattice: lack of discrimination of the two halves of the non-palindromic DNA sequence results in a pseudo-symmetric structure, with the A[16] element apparent in both halves. (b) Precise orientation of the non-palindromic DNA sequence in the crystal lattice leads to a unique structure in which the A[16] element (shown in black) is observed only in one half of the structure. Crystal packing and unit cell (black rectangle) are schematic and are not an accurate reflection of the true crystal lattice. (c) Stereo view of a section of the composite omit map, contoured at 1.2 σ, showing base-pair 67 from within the MRE. One orientation of the DNA molecule (green) fits the map much better than the other (magenta).
Figure 3.
Figure 3. Overall comparison of the DNA structure of A[16] NCP and α-sat NCP. Partial regions of the DNA, that is, bp 1–74 (a) and bp 75–147 (b) are viewed down the superhelical axis. The DNA of A[16] NCP and α-sat NCP are colored in red and blue, respectively. The A[16] element (bp 36–51, orange) and Amt1 binding site (MRE; bp 66–74, green), and the region of highest rmsd between the A[16] NCP and α-sat NCP (bp 125–135, cyan) are indicated. (c) Detailed comparison of a minor groove within the A[16] element (bp 37–45) and the corresponding region in α-sat NCP. (d) Side view of the A[16] NCP. The poly(dA·dT) element (bp 36–51) is colored in orange; bp 125–135 is colored in cyan. (e) Stereo view of a section of the |2F[o]–F[c]| electron density map, calculated at 3.2 Å and contoured at 1.2 σ, showing the part of the A[16] element (bp 37–39). (f) Minor groove widths (calculated with 3DNA as described in Materials and Methods) are plotted against DNA residue number (upper panel). Values for A[16] NCP model and α-sat NCP model are colored in magenta and blue, respectively. The positions for the A[16] element (red bar) and MRE (green bar) are labeled. Equivalent regions on the other half of the DNA are shown by broken red and green bars, respectively. Asterisks indicate regions of largest minor groove width differences. The rmsds for the DNA in A[16] NCP versus that in α-sat NCP are plotted against the DNA residue number (lower panel). Plots for the two strands (bases 2–147 and 149–294) are colored in orange and cyan, respectively.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 361, 617-624) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21176878 S.Tan, and C.A.Davey (2011).
Nucleosome structural studies.
  Curr Opin Struct Biol, 21, 128-136.  
20399189 B.Wu, K.Mohideen, D.Vasudevan, and C.A.Davey (2010).
Structural insight into the sequence dependence of nucleosome positioning.
  Structure, 18, 528-536.
PDB code: 3lel
19858362 C.Vaillant, L.Palmeira, G.Chevereau, B.Audit, Y.d'Aubenton-Carafa, C.Thermes, and A.Arneodo (2010).
A novel strategy of transcription regulation by intragenic nucleosome ordering.
  Genome Res, 20, 59-67.  
20106816 I.Gabdank, D.Barash, and E.N.Trifonov (2010).
FineStr: a web server for single-base-resolution nucleosome positioning.
  Bioinformatics, 26, 845-846.  
21168769 R.C.Todd, and S.J.Lippard (2010).
Consequences of cisplatin binding on nucleosome structure and dynamics.
  Chem Biol, 17, 1334-1343.
PDB code: 3o62
20739938 R.D.Makde, J.R.England, H.P.Yennawar, and S.Tan (2010).
Structure of RCC1 chromatin factor bound to the nucleosome core particle.
  Nature, 467, 562-566.
PDB code: 3mvd
20133331 R.Wu, and H.Li (2010).
Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters.
  Genome Res, 20, 473-484.  
  20232938 S.M.West, R.Rohs, R.S.Mann, and B.Honig (2010).
Electrostatic interactions between arginines and the minor groove in the nucleosome.
  J Biomol Struct Dyn, 27, 861-866.  
19208466 E.Segal, and J.Widom (2009).
Poly(dA:dT) tracts: major determinants of nucleosome organization.
  Curr Opin Struct Biol, 19, 65-71.  
19234544 L.Kelbauskas, N.Woodbury, and D.Lohr (2009).
DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysis.
  Biochem Cell Biol, 87, 323-335.  
19701201 M.G.Poirier, E.Oh, H.S.Tims, and J.Widom (2009).
Dynamics and function of compact nucleosome arrays.
  Nat Struct Mol Biol, 16, 938-944.  
19289051 S.Balasubramanian, F.Xu, and W.K.Olson (2009).
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.
  Biophys J, 96, 2245-2260.  
19508739 T.E.Haran, and U.Mohanty (2009).
The unique structure of A-tracts and intrinsic DNA bending.
  Q Rev Biophys, 42, 41-81.  
19074952 Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, and C.D.Hsiao (2009).
The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
  Nucleic Acids Res, 37, 804-814.
PDB codes: 2vye 2vyf
18940663 B.Wu, and C.A.Davey (2008).
Platinum drug adduct formation in the nucleosome core alters nucleosome mobility but not positioning.
  Chem Biol, 15, 1023-1028.  
18461484 S.H.Leuba, S.P.Anand, J.M.Harp, and S.A.Khan (2008).
Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time.
  Chromosome Res, 16, 451-467.  
18424496 T.C.Bishop (2008).
Geometry of the nucleosomal DNA superhelix.
  Biophys J, 95, 1007-1017.  
18550805 T.N.Mavrich, I.P.Ioshikhes, B.J.Venters, C.Jiang, L.P.Tomsho, J.Qi, S.C.Schuster, I.Albert, and B.F.Pugh (2008).
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
  Genome Res, 18, 1073-1083.  
18989395 Y.Field, N.Kaplan, Y.Fondufe-Mittendorf, I.K.Moore, E.Sharon, Y.Lubling, J.Widom, and E.Segal (2008).
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.
  PLoS Comput Biol, 4, e1000216.  
17585938 M.Y.Tolstorukov, A.V.Colasanti, D.M.McCandlish, W.K.Olson, and V.B.Zhurkin (2007).
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning.
  J Mol Biol, 371, 725-738.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.