spacer
spacer

PDBsum entry 2kvm
Go to PDB code: 
protein Protein-protein interface(s) links
Transcription PDB id
2kvm

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
71 a.a. *
16 a.a. *
* Residue conservation analysis
PDB id:
2kvm
Name: Transcription
Title: Solution structure of the cbx7 chromodomain in complex with a h3k27me2 peptide
Structure: Chromobox protein homolog 7. Chain: a. Fragment: chromodomain. Engineered: yes. Histone h3 peptide (residues 15-30) with dimethylated lysine 27. Chain: b. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: cbx7, d15ertd417e. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
NMR struc: 20 models
Authors: K.L.Yap,L.Zeng,M.Zhou
Key ref: K.L.Yap et al. (2010). Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell, 38, 662-674. PubMed id: 20541999
Date:
17-Mar-10     Release date:   30-Jun-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8VDS3  (CBX7_MOUSE) -  Chromobox protein homolog 7 from Mus musculus
Seq:
Struc: 		158 a.a.
71 a.a.
Protein chain
No UniProt id for this chain
Struc: 16 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Mol Cell 38:662-674 (2010)
PubMed id: 20541999  
 
 
Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.
K.L.Yap, S.Li, A.M.Muñoz-Cabello, S.Raguz, L.Zeng, S.Mujtaba, J.Gil, M.J.Walsh, M.M.Zhou.
 
  ABSTRACT  
 
Expression of the INK4b/ARF/INK4a tumor suppressor locus in normal and cancerous cell growth is controlled by methylation of histone H3 at lysine 27 (H3K27me) as directed by the Polycomb group proteins. The antisense noncoding RNA ANRIL of the INK4b/ARF/INK4a locus is also important for expression of the protein-coding genes in cis, but its mechanism has remained elusive. Here we report that chromobox 7 (CBX7) within the polycomb repressive complex 1 binds to ANRIL, and both CBX7 and ANRIL are found at elevated levels in prostate cancer tissues. In concert with H3K27me recognition, binding to RNA contributes to CBX7 function, and disruption of either interaction impacts the ability of CBX7 to repress the INK4b/ARF/INK4a locus and control senescence. Structure-guided analysis reveals the molecular interplay between noncoding RNA and H3K27me as mediated by the conserved chromodomain. Our study suggests a mechanism by which noncoding RNA participates directly in epigenetic transcriptional repression.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23417068 F.Lai, U.A.Orom, M.Cesaroni, M.Beringer, D.J.Taatjes, G.A.Blobel, and R.Shiekhattar (2013).
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription.
  Nature, 494, 497-501.  
23132386 S.Guil, and M.Esteller (2012).
Cis-acting noncoding RNAs: friends and foes.
  Nat Struct Mol Biol, 19, 1068-1075.  
22659877 S.Guil, M.Soler, A.Portela, J.Carrère, E.Fonalleras, A.Gómez, A.Villanueva, and M.Esteller (2012).
Intronic RNAs mediate EZH2 regulation of epigenetic targets.
  Nat Struct Mol Biol, 19, 664-670.  
20965211 A.P.Beltrami, D.Cesselli, and C.A.Beltrami (2011).
At the stem of youth and health.
  Pharmacol Ther, 129, 3.  
21174538 A.Piunti, and D.Pasini (2011).
Epigenetic factors in cancer development: polycomb group proteins.
  Future Oncol, 7, 57-75.  
21330185 B.Zheng, and X.Chen (2011).
Dynamics of histone H3 lysine 27 trimethylation in plant development.
  Curr Opin Plant Biol, 14, 123-129.  
21221116 C.Beisel, and R.Paro (2011).
Silencing chromatin: comparing modes and mechanisms.
  Nat Rev Genet, 12, 123-135.  
21697827 E.L.van Dijk, C.L.Chen, Y.d'Aubenton-Carafa, S.Gourvennec, M.Kwapisz, V.Roche, C.Bertrand, M.Silvain, P.Legoix-Né, S.Loeillet, A.Nicolas, C.Thermes, and A.Morillon (2011).
XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.
  Nature, 475, 114-117.  
21047797 L.Kaustov, H.Ouyang, M.Amaya, A.Lemak, N.Nady, S.Duan, G.A.Wasney, Z.Li, M.Vedadi, M.Schapira, J.Min, and C.H.Arrowsmith (2011).
Recognition and specificity determinants of the human cbx chromodomains.
  J Biol Chem, 286, 521-529.
PDB codes: 2l11 2l12 2l1b 3fdt 3gv6 3h91 3i90 3i91
  20799281 M.C.Trask, and J.Mager (2011).
Complexity of polycomb group function: diverse mechanisms of target specificity.
  J Cell Physiol, 226, 1719-1721.  
21487702 M.S.Cunnington, and B.Keavney (2011).
Genetic mechanisms mediating atherosclerosis susceptibility at the chromosome 9p21 locus.
  Curr Atheroscler Rep, 13, 193-201.  
21558279 M.U.Kaikkonen, M.T.Lam, and C.K.Glass (2011).
Non-coding RNAs as regulators of gene expression and epigenetics.
  Cardiovasc Res, 90, 430-440.  
21423274 M.Yun, J.Wu, J.L.Workman, and B.Li (2011).
Readers of histone modifications.
  Cell Res, 21, 564-578.  
21307941 O.Harismendy, D.Notani, X.Song, N.G.Rahim, B.Tanasa, N.Heintzman, B.Ren, X.D.Fu, E.J.Topol, M.G.Rosenfeld, and K.A.Frazer (2011).
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response.
  Nature, 470, 264-268.  
21112873 P.P.Amaral, M.B.Clark, D.K.Gascoigne, M.E.Dinger, and J.S.Mattick (2011).
lncRNAdb: a reference database for long noncoding RNAs.
  Nucleic Acids Res, 39, D146-D151.  
21414485 R.A.Young (2011).
Control of the embryonic stem cell state.
  Cell, 144, 940-954.  
21248841 R.Margueron, and D.Reinberg (2011).
The Polycomb complex PRC2 and its mark in life.
  Nature, 469, 343-349.  
21941284 S.B.Baylin, and P.A.Jones (2011).
A decade of exploring the cancer epigenome - biological and translational implications.
  Nat Rev Cancer, 11, 726-734.  
21151178 Y.Kotake, T.Nakagawa, K.Kitagawa, S.Suzuki, N.Liu, M.Kitagawa, and Y.Xiong (2011).
Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene.
  Oncogene, 30, 1956-1962.  
21151960 C.E.Burd, W.R.Jeck, Y.Liu, H.K.Sanoff, Z.Wang, and N.E.Sharpless (2010).
Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk.
  PLoS Genet, 6, e1001233.  
20864489 D.C.Crossman (2010).
SNPs and coronary angiography: can vascular biology be done from angiograms?
  Eur Heart J, 31, 2977-2979.  
21172659 J.Zhao, T.K.Ohsumi, J.T.Kung, Y.Ogawa, D.J.Grau, K.Sarma, J.J.Song, R.E.Kingston, M.Borowsky, and J.T.Lee (2010).
Genome-wide identification of polycomb-associated RNAs by RIP-seq.
  Mol Cell, 40, 939-953.  
20923397 K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
  Crit Rev Biochem Mol Biol, 45, 488-505.  
20616255 M.G.Guenther, and R.A.Young (2010).
Transcription. Repressive transcription.
  Science, 329, 150-151.  
20729297 M.Huarte, and J.L.Rinn (2010).
Large non-coding RNAs: missing links in cancer?
  Hum Mol Genet, 19, R152-R161.  
20804967 M.Sauvageau, and G.Sauvageau (2010).
Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer.
  Cell Stem Cell, 7, 299-313.  
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.

 

spacer
spacer