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PDBsum entry 3c9c
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protein metals Protein-protein interface(s) links
Transcription repressor PDB id
3c9c

 

 

 

 

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Contents
Protein chains
380 a.a. *
11 a.a. *
Metals
_CD ×7
* Residue conservation analysis
PDB id:
3c9c
Name: Transcription repressor
Title: Structural basis of histone h4 recognition by p55
Structure: Chromatin assembly factor 1 p55 subunit. Chain: a. Synonym: probable histone-binding protein caf1, caf-1 p55 subunit, dcaf-1, nucleosome-remodeling factor 55 kda subunit, nurf-55. Engineered: yes. Histone h4, 27-residue peptide. Chain: b. Fragment: unp residues 16-42. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: caf1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence is found naturally in drosophila melanogaster.
Resolution:
3.20Å     R-factor:   0.203     R-free:   0.242
Authors: J.J.Song,J.D.Garlick,R.E.Kingston
Key ref: J.J.Song et al. (2008). Structural basis of histone H4 recognition by p55. Genes Dev, 22, 1313-1318. PubMed id: 18443147
Date:
15-Feb-08     Release date:   13-May-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q24572  (CAF1_DROME) -  Chromatin assembly factor 1 p55 subunit from Drosophila melanogaster
Seq:
Struc: 		430 a.a.
380 a.a.
Protein chain
Pfam   ArchSchema ?
P84040  (H4_DROME) -  Histone H4 from Drosophila melanogaster
Seq:
Struc: 		103 a.a.
11 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Genes Dev 22:1313-1318 (2008)
PubMed id: 18443147  
 
 
Structural basis of histone H4 recognition by p55.
J.J.Song, J.D.Garlick, R.E.Kingston.
 
  ABSTRACT  
 
p55 is a common component of many chromatin-modifying complexes and has been shown to bind to histones. Here, we present a crystal structure of Drosophila p55 bound to a histone H4 peptide. p55, a predicted WD40 repeat protein, recognizes the first helix of histone H4 via a binding pocket located on the side of a beta-propeller structure. The pocket cannot accommodate the histone fold of H4, which must be altered to allow p55 binding. Reconstitution experiments show that the binding pocket is important to the function of p55-containing complexes. These data demonstrate that WD40 repeat proteins use various surfaces to direct the modification of histones.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23178455 W.Zhang, M.Tyl, R.Ward, F.Sobott, J.Maman, A.S.Murthy, A.A.Watson, O.Fedorov, A.Bowman, T.Owen-Hughes, H.El Mkami, N.V.Murzina, D.G.Norman, and E.D.Laue (2013).
Structural plasticity of histones H3-H4 facilitates their allosteric exchange between RbAp48 and ASF1.
  Nat Struct Mol Biol, 20, 29-35.  
21468892 C.Xu, and J.Min (2011).
Structure and function of WD40 domain proteins.
  Protein Cell, 2, 202-214.
PDB codes: 3e0c 3fm0 3i2n 3ow8
21549310 F.W.Schmitges, A.B.Prusty, M.Faty, A.Stützer, G.M.Lingaraju, J.Aiwazian, R.Sack, D.Hess, L.Li, S.Zhou, R.D.Bunker, U.Wirth, T.Bouwmeester, A.Bauer, N.Ly-Hartig, K.Zhao, H.Chan, J.Gu, H.Gut, W.Fischle, J.Müller, and N.H.Thomä (2011).
Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks.
  Mol Cell, 42, 330-341.
PDB codes: 2yb8 2yba
21240272 J.Oberoi, L.Fairall, P.J.Watson, J.C.Yang, Z.Czimmerer, T.Kampmann, B.T.Goult, J.A.Greenwood, J.T.Gooch, B.C.Kallenberger, L.Nagy, D.Neuhaus, and J.W.Schwabe (2011).
Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery.
  Nat Struct Mol Biol, 18, 177-184.
PDB codes: 2l5g 2xtc 2xtd 2xte
21248841 R.Margueron, and D.Reinberg (2011).
The Polycomb complex PRC2 and its mark in life.
  Nature, 469, 343-349.  
21047798 S.Lejon, S.Y.Thong, A.Murthy, S.AlQarni, N.V.Murzina, G.A.Blobel, E.D.Laue, and J.P.Mackay (2011).
Insights into association of the NuRD complex with FOG-1 from the crystal structure of an RbAp48·FOG-1 complex.
  J Biol Chem, 286, 1196-1203.
PDB code: 2xu7
20520775 A.Aslam, and C.Logie (2010).
Histone H3 serine 57 and lysine 56 interplay in transcription elongation and recovery from S-phase stress.
  PLoS One, 5, e10851.  
19914933 A.Bowman, R.Ward, H.El-Mkami, T.Owen-Hughes, and D.G.Norman (2010).
Probing the (H3-H4)2 histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling.
  Nucleic Acids Res, 38, 695-707.  
20444609 C.Das, J.K.Tyler, and M.E.Churchill (2010).
The histone shuffle: histone chaperones in an energetic dance.
  Trends Biochem Sci, 35, 476-489.  
20451393 C.U.Stirnimann, E.Petsalaki, R.B.Russell, and C.W.Müller (2010).
WD40 proteins propel cellular networks.
  Trends Biochem Sci, 35, 565-574.  
20974918 C.Xu, C.Bian, W.Yang, M.Galka, H.Ouyang, C.Chen, W.Qiu, H.Liu, A.E.Jones, F.MacKenzie, P.Pan, S.S.Li, H.Wang, and J.Min (2010).
Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2).
  Proc Natl Acad Sci U S A, 107, 19266-19271.
PDB codes: 3jpx 3jzg 3jzh 3jzn 3k26 3k27
20953179 E.I.Campos, J.Fillingham, G.Li, H.Zheng, P.Voigt, W.H.Kuo, H.Seepany, Z.Gao, L.A.Day, J.F.Greenblatt, and D.Reinberg (2010).
The program for processing newly synthesized histones H3.1 and H4.
  Nat Struct Mol Biol, 17, 1343-1351.  
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.  
20141833 M.Ransom, B.K.Dennehey, and J.K.Tyler (2010).
Chaperoning histones during DNA replication and repair.
  Cell, 140, 183-195.  
20080577 M.Shuaib, K.Ouararhni, S.Dimitrov, and A.Hamiche (2010).
HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres.
  Proc Natl Acad Sci U S A, 107, 1349-1354.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
20008334 T.Suganuma, and J.L.Workman (2010).
WD40 repeats arrange histone tails for spreading of silencing.
  J Mol Cell Biol, 2, 81-83.  
19927323 X.H.Wu, H.Zhang, and Y.D.Wu (2010).
Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: a statistical and theoretical study.
  Proteins, 78, 1186-1194.  
19234478 A.V.Probst, E.Dunleavy, and G.Almouzni (2009).
Epigenetic inheritance during the cell cycle.
  Nat Rev Mol Cell Biol, 10, 192-206.  
19410545 E.M.Dunleavy, D.Roche, H.Tagami, N.Lacoste, D.Ray-Gallet, Y.Nakamura, Y.Daigo, Y.Nakatani, and G.Almouzni-Pettinotti (2009).
HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres.
  Cell, 137, 485-497.  
19738629 J.A.Simon, and R.E.Kingston (2009).
Mechanisms of polycomb gene silencing: knowns and unknowns.
  Nat Rev Mol Cell Biol, 10, 697-708.  
19345089 J.Müller, and P.Verrijzer (2009).
Biochemical mechanisms of gene regulation by polycomb group protein complexes.
  Curr Opin Genet Dev, 19, 150-158.  
19853237 W.El-Sayed, D.A.Parry, R.C.Shore, M.Ahmed, H.Jafri, Y.Rashid, S.Al-Bahlani, S.Al Harasi, J.Kirkham, C.F.Inglehearn, and A.J.Mighell (2009).
Mutations in the beta propeller WDR72 cause autosomal-recessive hypomaturation amelogenesis imperfecta.
  Am J Hum Genet, 85, 699-705.  
18782834 H.Wang, S.T.Walsh, and M.R.Parthun (2008).
Expanded binding specificity of the human histone chaperone NASP.
  Nucleic Acids Res, 36, 5763-5772.  
18840606 J.J.Song, and R.E.Kingston (2008).
WDR5 interacts with mixed lineage leukemia (MLL) protein via the histone H3-binding pocket.
  J Biol Chem, 283, 35258-35264.
PDB code: 3emh
19026781 R.Margueron, G.Li, K.Sarma, A.Blais, J.Zavadil, C.L.Woodcock, B.D.Dynlacht, and D.Reinberg (2008).
Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms.
  Mol Cell, 32, 503-518.  
18483215 T.Suganuma, S.G.Pattenden, and J.L.Workman (2008).
Diverse functions of WD40 repeat proteins in histone recognition.
  Genes Dev, 22, 1265-1268.  
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.

 

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