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PDBsum entry 1u35

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protein dna_rna Protein-protein interface(s) links
Structural protein/DNA PDB id
1u35
Jmol
Contents
Protein chains
98 a.a. *
79 a.a. *
106 a.a. *
93 a.a. *
83 a.a. *
DNA/RNA
Waters ×105
* Residue conservation analysis
PDB id:
1u35
Name: Structural protein/DNA
Title: Crystal structure of the nucleosome core particle containing the histone domain of macroh2a
Structure: Alpha-satellite DNA. Chain: i, j. Engineered: yes. Histone h3.1. Chain: a, e. Synonym: h3/a, h3/c, h3/d, h3/f, h3/h, h3/i, h3/j, h3/k, h3/l. Engineered: yes. Hist1h4i protein.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090. Gene: h3fa, h3fc, h3fd, h3ff, h3fh, h3fi, h3fj, h3fk, h3fl.
Biol. unit: Decamer (from PQS)
Resolution:
3.00Å     R-factor:   0.206     R-free:   0.260
Authors: S.Chakravarthy,S.K.Gundimella,C.Caron,P.Y.Perche, J.R.Pehrson,S.Khochbin,K.Luger
Key ref: S.Chakravarthy et al. (2005). Structural characterization of the histone variant macroH2A. Mol Cell Biol, 25, 7616-7624. PubMed id: 16107708
Date:
20-Jul-04     Release date:   27-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P68433  (H31_MOUSE) -  Histone H3.1
Seq:
Struc:
136 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P62806  (H4_MOUSE) -  Histone H4
Seq:
Struc:
103 a.a.
79 a.a.
Protein chains
Pfam   ArchSchema ?
O75367  (H2AY_HUMAN) -  Core histone macro-H2A.1
Seq:
Struc:
372 a.a.
106 a.a.*
Protein chains
Pfam   ArchSchema ?
Q9D2U9  (H2B3A_MOUSE) -  Histone H2B type 3-A
Seq:
Struc:
126 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P62806  (H4_MOUSE) -  Histone H4
Seq:
Struc:
103 a.a.
83 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   7 terms 
  Biological process     regulation of gene silencing   6 terms 
  Biochemical function     protein binding     4 terms  

 

 
Mol Cell Biol 25:7616-7624 (2005)
PubMed id: 16107708  
 
 
Structural characterization of the histone variant macroH2A.
S.Chakravarthy, S.K.Gundimella, C.Caron, P.Y.Perche, J.R.Pehrson, S.Khochbin, K.Luger.
 
  ABSTRACT  
 
macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold region of macroH2A impact the structure and potentially the function of nucleosomes. The 1.6-A X-ray structure of the nonhistone region reveals an alpha/beta fold which has previously been found in a functionally diverse group of proteins. This region associates with histone deacetylases and affects the acetylation status of nucleosomes containing macroH2A. Thus, the unusual domain structure of macroH2A integrates independent functions that are instrumental in establishing a structurally and functionally unique chromatin domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21208404 A.Marathe, and M.Bansal (2011).
An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression.
  BMC Struct Biol, 11, 1.  
21364955 N.Friedman, M.Barzily-Rokni, S.Isaac, and A.Eden (2011).
The Histone H2A Variant MacroH2A1 Does Not Localize to the Centrosome.
  PLoS One, 6, e17262.  
21176878 S.Tan, and C.A.Davey (2011).
Nucleosome structural studies.
  Curr Opin Struct Biol, 21, 128-136.  
20132012 C.C.Chang, S.Gao, L.Y.Sung, G.N.Corry, Y.Ma, Z.P.Nagy, X.C.Tian, and T.P.Rasmussen (2010).
Rapid elimination of the histone variant MacroH2A from somatic cell heterochromatin after nuclear transfer.
  Cell Reprogram, 12, 43-53.  
20670405 I.Araya, G.Nardocci, J.Morales, M.Vera, A.Molina, and M.Alvarez (2010).
MacroH2A subtypes contribute antagonistically to the transcriptional regulation of the ribosomal cistron during seasonal acclimatization of the carp fish.
  Epigenetics Chromatin, 3, 14.  
20008927 M.J.Gamble, K.M.Frizzell, C.Yang, R.Krishnakumar, and W.L.Kraus (2010).
The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing.
  Genes Dev, 24, 21-32.  
19234519 A.A.Thambirajah, A.Li, T.Ishibashi, and J.Ausió (2009).
New developments in post-translational modifications and functions of histone H2A variants.
  Biochem Cell Biol, 87, 7.  
19052085 A.Chatterjee, M.A.Johnson, P.Serrano, B.Pedrini, J.S.Joseph, B.W.Neuman, K.Saikatendu, M.J.Buchmeier, P.Kuhn, and K.Wüthrich (2009).
Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.
  J Virol, 83, 1823-1836.
PDB codes: 2jzd 2jze 2jzf 2rnk
19395054 E.Park, and D.E.Griffin (2009).
The nsP3 macro domain is important for Sindbis virus replication in neurons and neurovirulence in mice.
  Virology, 388, 305-314.  
19386706 H.Malet, B.Coutard, S.Jamal, H.Dutartre, N.Papageorgiou, M.Neuvonen, T.Ahola, N.Forrester, E.A.Gould, D.Lafitte, F.Ferron, J.Lescar, A.E.Gorbalenya, X.de Lamballerie, and B.Canard (2009).
The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket.
  J Virol, 83, 6534-6545.
PDB codes: 3gpg 3gpo 3gpq 3gqe 3gqo
19436709 J.Tan, C.Vonrhein, O.S.Smart, G.Bricogne, M.Bollati, Y.Kusov, G.Hansen, J.R.Mesters, C.L.Schmidt, and R.Hilgenfeld (2009).
The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes.
  PLoS Pathog, 5, e1000428.
PDB codes: 2w2g 2wct
19734898 M.Buschbeck, I.Uribesalgo, I.Wibowo, P.Rué, D.Martin, A.Gutierrez, L.Morey, R.Guigó, H.López-Schier, and L.Di Croce (2009).
The histone variant macroH2A is an epigenetic regulator of key developmental genes.
  Nat Struct Mol Biol, 16, 1074-1079.  
  19177346 Y.Piotrowski, G.Hansen, A.L.Boomaars-van der Zanden, E.J.Snijder, A.E.Gorbalenya, and R.Hilgenfeld (2009).
Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property.
  Protein Sci, 18, 6.
PDB codes: 3ejf 3ejg 3eke
17957772 C.R.Clapier, S.Chakravarthy, C.Petosa, C.Fernández-Tornero, K.Luger, and C.W.Müller (2008).
Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer.
  Proteins, 71, 1-7.
PDB code: 2pyo
18424496 T.C.Bishop (2008).
Geometry of the nucleosomal DNA superhelix.
  Biophys J, 95, 1007-1017.  
17570398 D.A.Nusinow, J.A.Sharp, A.Morris, S.Salas, K.Plath, and B.Panning (2007).
The histone domain of macroH2A1 contains several dispersed elements that are each sufficient to direct enrichment on the inactive X chromosome.
  J Mol Biol, 371, 11-18.  
16540311 C.L.Woodcock (2006).
Chromatin architecture.
  Curr Opin Struct Biol, 16, 213-220.  
16428466 C.M.Doyen, W.An, D.Angelov, V.Bondarenko, F.Mietton, V.M.Studitsky, A.Hamiche, R.G.Roeder, P.Bouvet, and S.Dimitrov (2006).
Mechanism of polymerase II transcription repression by the histone variant macroH2A.
  Mol Cell Biol, 26, 1156-1164.  
16506092 K.Luger (2006).
Dynamic nucleosomes.
  Chromosome Res, 14, 5.  
17158748 K.Ouararhni, R.Hadj-Slimane, S.Ait-Si-Ali, P.Robin, F.Mietton, A.Harel-Bellan, S.Dimitrov, and A.Hamiche (2006).
The histone variant mH2A1.1 interferes with transcription by down-regulating PARP-1 enzymatic activity.
  Genes Dev, 20, 3324-3336.  
16738309 L.N.Changolkar, and J.R.Pehrson (2006).
macroH2A1 histone variants are depleted on active genes but concentrated on the inactive X chromosome.
  Mol Cell Biol, 26, 4410-4420.  
17036053 M.Agelopoulos, and D.Thanos (2006).
Epigenetic determination of a cell-specific gene expression program by ATF-2 and the histone variant macroH2A.
  EMBO J, 25, 4843-4853.  
17092350 M.Ducasse, and M.A.Brown (2006).
Epigenetic aberrations and cancer.
  Mol Cancer, 5, 60.  
16506096 S.A.Grigoryev, Y.A.Bulynko, and E.Y.Popova (2006).
The end adjusts the means: heterochromatin remodelling during terminal cell differentiation.
  Chromosome Res, 14, 53-69.  
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 codes are shown on the right.