Citations in PubMed

Primary Citation PubMed: 11859155 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila.

(2005) PLoS Genet 1

PubMed: 16103923 | PubMedCentral: PMC1183528 | DOI: 10.1371/journal.pgen.0010009

The Molecular Modeling Database (MMDB; http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml ) accession numbers of the proteins discussed in this paper are H3K9me (19011, PDB 1KNE) and HP1 β ... hadow domain dimer (13286, PDB 1DZ1).

Publication Year: 2005


Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.

(2009) Nucleic Acids Res 37

PubMed: 19233876 | PubMedCentral: PMC2673432 | DOI: 10.1093/nar/gkp086

( C ) Surface representation of the HP1 and H3K9me3 complex structure (PDB 1KNE).

Publication Year: 2009


Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.

(2010) Nat Struct Mol Biol 17

PubMed: 20657587 | PubMedCentral: PMC2924628 | DOI: 10.1038/nsmb.1856

References 1 Alekseyenko AA Cell 2008 134 599 609 18724933 2 Straub T Grimaud C Gilfillan GD Mitterweger A Becker PB PLoS Genet 2008 4 e1000302 19079572 3 Smith ER Mol Cell Biol 2005 25 9175 9188 1622... 571 4 Li X Wu L Corsa CA Kunkel S Dou Y Mol Cell 2009 36 290 301 19854137 5 Lucchesi JC Curr Opin Genet Dev 2009 19 550 556 19880310 6 Akhtar A Zink D Becker PB Nature 2000 407 405 409 11014199 7 Nielsen PR J Biol Chem 2005 280 32326 32331 15964847 8 Sural TH Nat Struct Mol Biol 2008 15 1318 1325 19029895 9 Buscaino A Legube G Akhtar A EMBO Rep 2006 7 531 538 16547465 10 Jacobs SA Khorasanizadeh S Science 2002 295 2080 2083 11859155 11 Kim J EMBO Rep 2006 7 397 403 16415788 12 Chandra V Nature 2008 456 350 356 19043829 13 Yang H Mizzen CA Biochem Cell Biol 2009 87 151 161 19234531 14 Nishioka K Mol Cell 2002 9 1201 1213 12086618 15 Robinson H Nature 1998 392 202 205 9515968 16 Flanagan JF Nature 2005 438 1181 1185 16372014 17 Li B Carey M Workman JL Cell 2007 128 707 719 17320508 18 Barski A Cell 2007 129 823 837 17512414 19 Trojer P Reinberg D Cell Cycle 2008 7 578 585 18256536 20 Schalch T Duda S Sargent DF Richmond TJ Nature 2005 436 138 141 16001076 Figure 1 MSL3 chromodomain structure and specificity ( a ) Superposition of the Drosophila MSL3 with MOF (PDB: 2BUD) and HP1 bound to a H3K9me3 peptide (PDB:1KNE).

Publication Year: 2010


ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome.

(2011) Nat Struct Mol Biol 18

PubMed: 21666679 | PubMedCentral: PMC3130887 | DOI: 10.1038/nsmb.2062

For instance, H3 segments Gln5–Ser10, Lys4–Ser10, and Ala7–Gly13 were reported to be responsible for H3 binding by the HP1 chromodomain 33 (PDB code: 1KNE), the CHP1 chromodoma... n 34 (3G7L), and the GLP ankyrin repeat 32 (3B95), respectively ( Supplementary Fig. 7 ).

Publication Year: 2011


Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails.

(2011) BMC Biochem 12

PubMed: 21884582 | PubMedCentral: PMC3176149 | DOI: 10.1186/1471-2091-12-48

Trying to understand that difference, we superimposed the structures of HP1ß (pdb entry 1KNE ) [ 35 ] and MPP8 Chromo domain (pdb entry 3QO2 ) [ 13 ] in complex with H3K9me3 peptides and compa... ed the distances of unmodified R8 in the peptides to the nearest side chain atoms of the Chromo domains, which are E23 in HP1ß and E97 in MPP8 (Figure 2 ).

For a description of the figure see legend of panel A. In the structure of HP1ß bound to the H3K9me3 peptide (pdb entry 1KNE ) [ 35 ] (Figure 2 ), E23 is the only residue that closely approaches R8.

Figure 2 Superposition of the HP1ß (pdb entry 1KNE ) (dark green) and MPP8 Chromo domains (pdb entry 3QO2 ) (red) in complex with H3K9me3 peptides (light green for HP1 and orange for MPP8) .

Publication Year: 2011


Quantitative assessment of protein interaction with methyl-lysine analogues by hybrid computational and experimental approaches.

(2012) ACS Chem Biol 7

PubMed: 21991995 | PubMedCentral: PMC3265130 | DOI: 10.1021/cb200363r

Table 1 Measured and Calculated Binding Free Energy Differences (ΔΔ G ) of Interaction of the Indicated Proteins/Domains with Different Methylated Histone Tail Peptides protein PDB dom... in site method a K d (Kme) [μM] Δ G (Kme) [kJ/mol] K d (K C me) [μM] Δ G (K C me) [kJ/mol] ΔΔ G (exp) [kJ/mol] ΔΔ G (calc) [kJ/mol] Su(Var)205 1kne Chromo H3K9me3 ITC 0.3 ± 0.0 –37.6 ± 0.2 1.6 ± 0.1 –33.1 ± 0.2 4.5 ± 0.2 7.3 ± 0.4 ING1 2qic PHD finger H3K4me3 FP 16.2 ± 4.4 –27.3 ± 0.7 11.4 ± 2.3 –28.2 ± 0.5 –0.9 ± 0.8 –0.6 ± 0.4 L3MBTL1 2rhy 3xMBT H4K20me1 FP 6.2 ± 0.5 –29.7 ± 0.2 48.2 ± 3.0 –24.6 ± 0.2 5.1 ± 0.3 6.1 ± 0.5 ICBP90 3db3 pseudo Tudor H3K9me3 FP 0.4 ± 0.1 –36.7 ± 0.5 0.4 ± 0.1 –36.7 ± 0.7 0.0 ± 0.8 –1.2 ± 0.3 53BP1 2ig0 Tudor H4K20me2 FP 18.1 ± 2.8 –27.0 ± 0.4 b b c 2.7 ± 0.4 hHP1α(CBX5) 3dm1 Chromo H3K9me3             7.3 ± 0.4 hHP1β(CBX1)   Chromo H3K9me3 FP 1.9 ± 0.5 –32.7 ± 0.7 11.6 ± 3.9 –28.2 ± 0.8 4.6 ± 1.1   hHP1γ(CBX3) 3fdt Chromo G9aK165me3             7.3 ± 0.4 a Apparent molar dissociation constants ( K d ) for the different methyl-lysine binding domains were derived from isothermal calorimetry (ITC) or fluorescence polarization (FP) measurements for methyl-lysine (Kme) and methyl-lysine analogues (K C me) containing peptides.

Figure 2 Structural details of methyl-lysine (derived from the PDB entries, in gray) and corresponding methyl-lysine analogues (in purple with the sulfur in yellow) containing BD*pep complexes as used for the λ = 0 and λ = 1 states of the calculation are depicted for (a) Su(Var)205 Chromo domain/H3K9me3 (PDB code 1kne ), (b) L3MBTL1 3xMBT/H4K20me1 (PDB code 2rhy ), (c) ING1 PHD finger/H3K4me3 (PDB code 2qic ), and (d) ICBP90 pseudo Tudor/H3K9me3 (PDB code 3db3 ).

Publication Year: 2012


Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation.

(2012) Nat Struct Mol Biol 19

PubMed: 23022729 | PubMedCentral: PMC3492551 | DOI: 10.1038/nsmb.2391

A comparison of crystal structures of the UHRF1 TTD (PDB: 3DB3 20 ) ( Fig. 2e ), MPP8 chromodomain (PDB: 3QO2 31 ), and HP1α chromodomain (PDB: 1KNE 32 ) in complex with H3K9me3 peptides ident... fied a conserved, negatively charged glutamate residue in similar orientation and proximity (less than 3Å) to H3S10 as Asn147 of the UHRF1 TTD.

Publication Year: 2012


Crystal structure of the human SUV39H1 chromodomain and its recognition of histone H3K9me2/3.

(2012) PLoS One 7

PubMed: 23285239 | PubMedCentral: PMC3532415 | DOI: 10.1371/journal.pone.0052977

The structures of human SUV39H1 and Drosophila melanogaster HP1 (PDB: 1KNE) chromodomains are aligned and shown in magenta and cyan, respectively.

The structure was solved by molecular replacement using the crystal structure of the chromo domain of HP1 from Drosophila melanogaster (PDB 1KNE) as a search model and the program Phaser as implemented in the Phenix program suite [32] , [33] .

The Z-score and RMSD between the SUV39H1 chromodomain and the Drosophila HP1 chromodomain (PDB code 1KNE) are 9.4 and 1.0 Å, respectively, which demonstrates structure conservation between the two structures.

B: human MPP8 chromodomain (PDB ID: 3R93) C: Drosophila HP1 chromodomain (PDB ID: 1KNE).

Publication Year: 2012


Structural plasticity in human heterochromatin protein 1?.

(2013) PLoS One 8

PubMed: 23585859 | PubMedCentral: PMC3621757 | DOI: 10.1371/journal.pone.0060887

Upon interaction with methylated histone H3, residues L58–D59 are stabilized in a well-ordered intermolecular β-sandwich, as shown for CD of hHP1α (PDB code: 3FDT [6] , display... d in figure 5C in comparison with 3F2U structure), hHP1β (PDB code: 1GUW [7] ) and dmHP1 (PDB code: 1KNE [5] ).

Publication Year: 2013