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PDBsum entry 1e6i

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protein ligands links
Gene regulation PDB id
1e6i
Jmol
Contents
Protein chain
111 a.a. *
Ligands
ALA-ALY-ARG-HIS-
ARG-LYS
Waters ×109
* Residue conservation analysis
PDB id:
1e6i
Name: Gene regulation
Title: Bromodomain from gcn5 complexed with acetylated h4 peptide
Structure: Transcriptional activator gcn5. Chain: a. Fragment: bromodomain. Engineered: yes. Histone h4. Chain: p. Fragment: acetylated tail, residues 16-30. Other_details: lysine 16 is acetylated on nz
Source: Saccharomyces cerevisiae. Organism_taxid: 4932. Gene: gcn5. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
1.87Å     R-factor:   0.187     R-free:   0.209
Authors: D.J.Owen,A.A.Travers,P.R.Evans
Key ref:
D.J.Owen et al. (2000). The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO J, 19, 6141-6149. PubMed id: 11080160 DOI: 10.1093/emboj/19.22.6141
Date:
18-Aug-00     Release date:   24-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q03330  (GCN5_YEAST) -  Histone acetyltransferase GCN5
Seq:
Struc:
439 a.a.
111 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.48  - Histone acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetyl-CoA + [histone] = CoA + acetyl-[histone]
Acetyl-CoA
+ [histone]
= CoA
+ acetyl-[histone]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1093/emboj/19.22.6141 EMBO J 19:6141-6149 (2000)
PubMed id: 11080160  
 
 
The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p.
D.J.Owen, P.Ornaghi, J.C.Yang, N.Lowe, P.R.Evans, P.Ballario, D.Neuhaus, P.Filetici, A.A.Travers.
 
  ABSTRACT  
 
The bromodomain is an approximately 110 amino acid module found in histone acetyltransferases and the ATPase component of certain nucleosome remodelling complexes. We report the crystal structure at 1.9 A resolution of the Saccharomyces cerevisiae Gcn5p bromodomain complexed with a peptide corresponding to residues 15-29 of histone H4 acetylated at the zeta-N of lysine 16. We show that this bromodomain preferentially binds to peptides containing an N:-acetyl lysine residue. Only residues 16-19 of the acetylated peptide interact with the bromodomain. The primary interaction is the N:-acetyl lysine binding in a cleft with the specificity provided by the interaction of the amide nitrogen of a conserved asparagine with the oxygen of the acetyl carbonyl group. A network of water-mediated H-bonds with protein main chain carbonyl groups at the base of the cleft contributes to the binding. Additional side chain binding occurs on a shallow depression that is hydrophobic at one end and can accommodate charge interactions at the other. These findings suggest that the Gcn5p bromodomain may discriminate between different acetylated lysine residues depending on the context in which they are displayed.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Details of the peptide binding site. (A) Schematic view of interactions, with water molecules represented as W. (B) The N-acetyl lysine slot showing the ring of water molecules around the acetyl group at the base of the slot, and the hydrophobic walls left and right. (C) The binding groove for the (K + 2) and (K + 3) peptide residues lies across the 405–408 loop between [B] and [C]. His(K + 2) packs against Phe367, and Arg(K + 3) forms hydrogen bonds back to the protein backbone. The peptide backbone forms four hydrogen bonds to the protein, three of them via water molecules.
Figure 6.
Figure 6 The N -acetyl lysine binding site, showing electron density from the final 2mF[o] – DF[c] map. Nitrogen atoms are black and oxygen atoms are grey. The acetyl group is surrounded by a ring of water molecules (grey balls) at the base of the slot, and the carbonyl oxygen of the acetyl forms a hydrogen bond to the side chain of Asn407. An unacetylated lysine could not form these hydrogen bonds, and would introduce an unpaired charge into the slot.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 6141-6149) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors.
  Chem Biol, 18, 495-507.
PDB code: 3aqa
20536830 A.Nakamura, K.Kawakami, F.Kametani, H.Nakamoto, and S.Goto (2010).
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20862720 D.Schwarzer (2010).
Chemical tools in chromatin research.
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20459718 I.Tirosh, N.Sigal, and N.Barkai (2010).
Widespread remodeling of mid-coding sequence nucleosomes by Isw1.
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20923397 K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
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20871596 P.Filippakopoulos, J.Qi, S.Picaud, Y.Shen, W.B.Smith, O.Fedorov, E.M.Morse, T.Keates, T.T.Hickman, I.Felletar, M.Philpott, S.Munro, M.R.McKeown, Y.Wang, A.L.Christie, N.West, M.J.Cameron, B.Schwartz, T.D.Heightman, N.La Thangue, C.A.French, O.Wiest, A.L.Kung, S.Knapp, and J.E.Bradner (2010).
Selective inhibition of BET bromodomains.
  Nature, 468, 1067-1073.
PDB codes: 3mxf 3oni
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
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Biochemical profiling of histone binding selectivity of the yeast bromodomain family.
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20048151 T.Umehara, Y.Nakamura, M.K.Jang, K.Nakano, A.Tanaka, K.Ozato, B.Padmanabhan, and S.Yokoyama (2010).
Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.
  J Biol Chem, 285, 7610-7618.
PDB codes: 2dvq 2dvr 2dvs
20393127 Y.Akai, N.Adachi, Y.Hayashi, M.Eitoku, N.Sano, R.Natsume, N.Kudo, M.Tanokura, T.Senda, and M.Horikoshi (2010).
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PDB code: 3aad
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A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.
  Mol Cell Biol, 29, 4604-4611.  
19505939 C.Zang, D.E.Schones, C.Zeng, K.Cui, K.Zhao, and W.Peng (2009).
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
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19828451 F.Vollmuth, W.Blankenfeldt, and M.Geyer (2009).
Structures of the dual bromodomains of the P-TEFb-activating protein Brd4 at atomic resolution.
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PDB codes: 3jvj 3jvk 3jvl 3jvm
19794495 J.Morinière, S.Rousseaux, U.Steuerwald, M.Soler-López, S.Curtet, A.L.Vitte, J.Govin, J.Gaucher, K.Sadoul, D.J.Hart, J.Krijgsveld, S.Khochbin, C.W.Müller, and C.Petosa (2009).
Cooperative binding of two acetylation marks on a histone tail by a single bromodomain.
  Nature, 461, 664-668.
PDB codes: 2wp1 2wp2
19084573 M.Thompson (2009).
Polybromo-1: the chromatin targeting subunit of the PBAF complex.
  Biochimie, 91, 309-319.  
  19736624 R.Sanchez, and M.M.Zhou (2009).
The role of human bromodomains in chromatin biology and gene transcription.
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19103755 S.Guelman, K.Kozuka, Y.Mao, V.Pham, M.J.Solloway, J.Wang, J.Wu, J.R.Lill, and J.Zha (2009).
The double-histone-acetyltransferase complex ATAC is essential for mammalian development.
  Mol Cell Biol, 29, 1176-1188.  
19218239 S.Li, and M.A.Shogren-Knaak (2009).
The Gcn5 bromodomain of the SAGA complex facilitates cooperative and cross-tail acetylation of nucleosomes.
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19523169 Y.Hayashi, T.Senda, N.Sano, and M.Horikoshi (2009).
Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network.
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18508185 C.Kupitz, R.Chandrasekaran, and M.Thompson (2008).
Kinetic analysis of acetylation-dependent Pb1 bromodomain-histone interactions.
  Biophys Chem, 136, 7.  
18400184 L.Zeng, Q.Zhang, G.Gerona-Navarro, N.Moshkina, and M.M.Zhou (2008).
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  Structure, 16, 643-652.
PDB codes: 2rnw 2rnx 2rny
18319736 M.M.Brent, and R.Marmorstein (2008).
Ankyrin for methylated lysines.
  Nat Struct Mol Biol, 15, 221-222.  
18837912 S.Awad, and A.H.Hassan (2008).
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18404694 S.Jessen, B.Gu, and X.Dai (2008).
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18539634 S.Padilla-Parra, N.Audugé, M.Coppey-Moisan, and M.Tramier (2008).
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Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms.
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Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability.
  Mol Cell Biol, 27, 4037-4048.  
17848202 H.Huang, J.Zhang, W.Shen, X.Wang, J.Wu, J.Wu, and Y.Shi (2007).
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  BMC Struct Biol, 7, 57.  
17512413 I.B.Dodd, M.A.Micheelsen, K.Sneppen, and G.Thon (2007).
Theoretical analysis of epigenetic cell memory by nucleosome modification.
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17337012 J.A.Daniel, and P.A.Grant (2007).
Multi-tasking on chromatin with the SAGA coactivator complexes.
  Mutat Res, 618, 135-148.  
17925393 M.A.Holbert, T.Sikorski, J.Carten, D.Snowflack, S.Hodawadekar, and R.Marmorstein (2007).
The human monocytic leukemia zinc finger histone acetyltransferase domain contains DNA-binding activity implicated in chromatin targeting.
  J Biol Chem, 282, 36603-36613.
PDB code: 2rc4
17200759 M.A.Zoroddu, M.Peana, and S.Medici (2007).
Multidimensional NMR spectroscopy for the study of histone H4-Ni(II) interaction.
  Dalton Trans, (), 379-384.  
17362198 M.D.Shahbazian, and M.Grunstein (2007).
Functions of site-specific histone acetylation and deacetylation.
  Annu Rev Biochem, 76, 75.  
17526728 M.Durant, and B.F.Pugh (2007).
NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome.
  Mol Cell Biol, 27, 5327-5335.  
17582821 M.Singh, G.M.Popowicz, M.Krajewski, and T.A.Holak (2007).
Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex.
  Chembiochem, 8, 1308-1316.
PDB code: 2grc
17340003 N.Jamonnak, D.G.Fatkins, L.Wei, and W.Zheng (2007).
N(epsilon)-methanesulfonyl-lysine as a non-hydrolyzable functional surrogate for N(epsilon)-acetyl-lysine.
  Org Biomol Chem, 5, 892-896.  
17618463 R.J.Tseng, K.R.Armstrong, X.Wang, and H.M.Chamberlin (2007).
The bromodomain protein LEX-1 acts with TAM-1 to modulate gene expression in C. elegans.
  Mol Genet Genomics, 278, 507-518.  
17694078 R.Murr, T.Vaissière, C.Sawan, V.Shukla, and Z.Herceg (2007).
Orchestration of chromatin-based processes: mind the TRRAP.
  Oncogene, 26, 5358-5372.  
17984965 S.D.Taverna, H.Li, A.J.Ruthenburg, C.D.Allis, and D.J.Patel (2007).
How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.
  Nat Struct Mol Biol, 14, 1025-1040.  
17934485 S.I.Kim, and E.H.Bresnick (2007).
Transcriptional control of erythropoiesis: emerging mechanisms and principles.
  Oncogene, 26, 6777-6794.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
17694091 S.Mujtaba, L.Zeng, and M.M.Zhou (2007).
Structure and acetyl-lysine recognition of the bromodomain.
  Oncogene, 26, 5521-5527.  
18025461 S.Ramón-Maiques, A.J.Kuo, D.Carney, A.G.Matthews, M.A.Oettinger, O.Gozani, and W.Yang (2007).
The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.
  Proc Natl Acad Sci U S A, 104, 18993-18998.
PDB codes: 2v83 2v85 2v86 2v87 2v88
17306844 V.K.Gangaraju, and B.Bartholomew (2007).
Mechanisms of ATP dependent chromatin remodeling.
  Mutat Res, 618, 3.  
17148447 Y.Nakamura, T.Umehara, K.Nakano, M.K.Jang, M.Shirouzu, S.Morita, H.Uda-Tochio, H.Hamana, T.Terada, N.Adachi, T.Matsumoto, A.Tanaka, M.Horikoshi, K.Ozato, B.Padmanabhan, and S.Yokoyama (2007).
Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4.
  J Biol Chem, 282, 4193-4201.  
17694077 Z.Nagy, and L.Tora (2007).
Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation.
  Oncogene, 26, 5341-5357.  
16648632 A.H.Hassan, S.Awad, and P.Prochasson (2006).
The Swi2/Snf2 bromodomain is required for the displacement of SAGA and the octamer transfer of SAGA-acetylated nucleosomes.
  J Biol Chem, 281, 18126-18134.  
16829979 B.T.Seet, I.Dikic, M.M.Zhou, and T.Pawson (2006).
Reading protein modifications with interaction domains.
  Nat Rev Mol Cell Biol, 7, 473-483.  
16265664 C.Peng, J.Zhou, H.Y.Liu, M.Zhou, L.L.Wang, Q.H.Zhang, Y.X.Yang, W.Xiong, S.R.Shen, X.L.Li, and G.Y.Li (2006).
The transcriptional regulation role of BRD7 by binding to acetylated histone through bromodomain.
  J Cell Biochem, 97, 882-892.  
16923967 D.G.Martin, K.Baetz, X.Shi, K.L.Walter, V.E.MacDonald, M.J.Wlodarski, O.Gozani, P.Hieter, and L.Howe (2006).
The Yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone H3.
  Mol Cell Biol, 26, 7871-7879.  
17121596 E.Agricola, L.Verdone, E.Di Mauro, and M.Caserta (2006).
H4 acetylation does not replace H3 acetylation in chromatin remodelling and transcription activation of Adr1-dependent genes.
  Mol Microbiol, 62, 1433-1446.  
16180204 F.Pizzitutti, A.Giansanti, P.Ballario, P.Ornaghi, P.Torreri, G.Ciccotti, and P.Filetici (2006).
The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment.
  J Mol Recognit, 19, 1-9.  
16461455 G.Da, J.Lenkart, K.Zhao, R.Shiekhattar, B.R.Cairns, and R.Marmorstein (2006).
Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes.
  Proc Natl Acad Sci U S A, 103, 2057-2062.
PDB code: 2fq3
16728978 H.Li, S.Ilin, W.Wang, E.M.Duncan, J.Wysocka, C.D.Allis, and D.J.Patel (2006).
Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
  Nature, 442, 91-95.
PDB codes: 2f6j 2f6n 2fsa 2fui 2fuu
16487697 H.Wurtele, and A.Verreault (2006).
Histone post-translational modifications and the response to DNA double-strand breaks.
  Curr Opin Cell Biol, 18, 137-144.  
17023429 L.Ooi, N.D.Belyaev, K.Miyake, I.C.Wood, and N.J.Buckley (2006).
BRG1 chromatin remodeling activity is required for efficient chromatin binding by repressor element 1-silencing transcription factor (REST) and facilitates REST-mediated repression.
  J Biol Chem, 281, 38974-38980.  
17030999 M.Chandy, J.L.Gutiérrez, P.Prochasson, and J.L.Workman (2006).
SWI/SNF displaces SAGA-acetylated nucleosomes.
  Eukaryot Cell, 5, 1738-1747.  
16623890 M.Peng, Y.Cui, Y.M.Bi, and S.J.Rothstein (2006).
AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis.
  Plant J, 46, 282-296.  
17081121 M.Singh, L.D'Silva, and T.A.Holak (2006).
DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein.
  Biol Chem, 387, 1469-1478.  
17014737 M.Yoshino, T.Mizutani, K.Yamada, T.Yazawa, H.Ogata-Kawata, T.Sekiguchi, T.Kajitani, and K.Miyamoto (2006).
Co-activator p120 is increased by gonadotropins in the rat ovary and enhances progesterone receptor activity.
  Reprod Biol Endocrinol, 4, 50.  
16954381 S.P.Sripathy, J.Stevens, and D.C.Schultz (2006).
The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression.
  Mol Cell Biol, 26, 8623-8638.  
16362936 S.Pantano, A.Marcello, A.Ferrari, D.Gaudiosi, A.Sabò, V.Pellegrini, F.Beltram, M.Giacca, and P.Carloni (2006).
Insights on HIV-1 Tat:P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations.
  Proteins, 62, 1062-1073.  
16275642 A.R.Colina, and D.Young (2005).
Raf60, a novel component of the Rpd3 histone deacetylase complex required for Rpd3 activity in Saccharomyces cerevisiae.
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16099183 C.A.Berkes, and S.J.Tapscott (2005).
MyoD and the transcriptional control of myogenesis.
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16135811 C.Carré, D.Szymczak, J.Pidoux, and C.Antoniewski (2005).
The histone H3 acetylase dGcn5 is a key player in Drosophila melanogaster metamorphosis.
  Mol Cell Biol, 25, 8228-8238.  
16227593 D.J.Eastburn, and M.Han (2005).
A gain-of-function allele of cbp-1, the Caenorhabditis elegans ortholog of the mammalian CBP/p300 gene, causes an increase in histone acetyltransferase activity and antagonism of activated Ras.
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The macro domain is an ADP-ribose binding module.
  EMBO J, 24, 1911-1920.
PDB codes: 2bfq 2bfr
15831453 H.Qiu, C.Hu, F.Zhang, G.J.Hwang, M.J.Swanson, C.Boonchird, and A.G.Hinnebusch (2005).
Interdependent recruitment of SAGA and Srb mediator by transcriptional activator Gcn4p.
  Mol Cell Biol, 25, 3461-3474.  
15577942 J.Li, R.Santoro, K.Koberna, and I.Grummt (2005).
The chromatin remodeling complex NoRC controls replication timing of rRNA genes.
  EMBO J, 24, 120-127.  
15959560 L.Verdone, M.Caserta, and E.Di Mauro (2005).
Role of histone acetylation in the control of gene expression.
  Biochem Cell Biol, 83, 344-353.  
15767660 M.D.Stewart, J.Li, and J.Wong (2005).
Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment.
  Mol Cell Biol, 25, 2525-2538.  
15951563 M.Fu, C.Wang, M.Rao, X.Wu, T.Bouras, X.Zhang, Z.Li, X.Jiao, J.Yang, A.Li, N.D.Perkins, B.Thimmapaya, A.L.Kung, A.Munoz, A.Giordano, M.P.Lisanti, and R.G.Pestell (2005).
Cyclin D1 represses p300 transactivation through a cyclin-dependent kinase-independent mechanism.
  J Biol Chem, 280, 29728-29742.  
16079223 N.Jambunathan, A.W.Martinez, E.C.Robert, N.B.Agochukwu, M.E.Ibos, S.L.Dugas, and D.Donze (2005).
Multiple bromodomain genes are involved in restricting the spread of heterochromatic silencing at the Saccharomyces cerevisiae HMR-tRNA boundary.
  Genetics, 171, 913-922.  
16246723 N.Macdonald, J.P.Welburn, M.E.Noble, A.Nguyen, M.B.Yaffe, D.Clynes, J.G.Moggs, G.Orphanides, S.Thomson, J.W.Edmunds, A.L.Clayton, J.A.Endicott, and L.C.Mahadevan (2005).
Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3.
  Mol Cell, 20, 199-211.
PDB codes: 2c1j 2c1n
15561719 T.Macfarlan, S.Kutney, B.Altman, R.Montross, J.Yu, and D.Chakravarti (2005).
Human THAP7 is a chromatin-associated, histone tail-binding protein that represses transcription via recruitment of HDAC3 and nuclear hormone receptor corepressor.
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15666348 X.de la Cruz, S.Lois, S.Sánchez-Molina, and M.A.Martínez-Balbás (2005).
Do protein motifs read the histone code?
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ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD-histone contacts.
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PDB code: 1jsp
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PDB code: 1jm4
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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.