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3N9L
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BU of 3n9l by Molmil
ceKDM7A from C.elegans, complex with H3K4me3 peptide and NOG
Descriptor: FE (II) ION, Histone H3 peptide, N-OXALYLGLYCINE, ...
Authors:Yang, Y, Hu, L, Wang, P, Hou, H, Chen, C.D, Xu, Y.
Deposit date:2010-05-31
Release date:2010-06-30
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.796 Å)
Cite:Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans
Cell Res., 20, 2010
2M3H
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BU of 2m3h by Molmil
Structure of Dido PHD domain
Descriptor: Death-inducer obliterator 1, ZINC ION
Authors:Santiveri, C.M, Perez-Canadillas, J.M, Jimenez, M.
Deposit date:2013-01-19
Release date:2013-08-07
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3.
J.Biomol.Nmr, 56, 2013
8VLF
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BU of 8vlf by Molmil
Crystal structure of Ash1L PHD finger in complex with histone H3K4me3
Descriptor: Histone H3.3C, Histone-lysine N-methyltransferase ASH1L, ZINC ION
Authors:Vann, K.R, Kutateladze, T.G.
Deposit date:2024-01-11
Release date:2025-03-19
Method:X-RAY DIFFRACTION (1.34 Å)
Cite:Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation.
Nat Commun, 16, 2025
3KQI
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BU of 3kqi by Molmil
crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide
Descriptor: CHLORIDE ION, GLYCEROL, H3K4Me3 peptide, ...
Authors:Wen, H, Li, J.Z, Song, T, Lu, M, Lee, M.
Deposit date:2009-11-17
Release date:2010-02-02
Last modified:2025-03-26
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.
J.Biol.Chem., 285, 2010
2K16
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BU of 2k16 by Molmil
Solution structure of the free TAF3 PHD domain
Descriptor: Transcription initiation factor TFIID subunit 3, ZINC ION
Authors:van Ingen, H, van Schaik, F.M.A, Wienk, H, Timmers, M, Boelens, R.
Deposit date:2008-02-22
Release date:2008-07-15
Last modified:2024-05-08
Method:SOLUTION NMR
Cite:Recognition of the H3K4me3 mark by the TAF3-PHD finger
To be Published
3N9P
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BU of 3n9p by Molmil
ceKDM7A from C.elegans, complex with H3K4me3K27me2 peptide and NOG
Descriptor: FE (II) ION, Histone H3 peptide, N-OXALYLGLYCINE, ...
Authors:Yang, Y, Hu, L, Wang, P, Hou, H, Chen, C.D, Xu, Y.
Deposit date:2010-05-31
Release date:2010-06-30
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.388 Å)
Cite:Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans
Cell Res., 20, 2010
3N9N
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ceKDM7A from C.elegans, complex with H3K4me3K9me2 peptide and NOG
Descriptor: FE (II) ION, Histone H3 peptide, N-OXALYLGLYCINE, ...
Authors:Yang, Y, Hu, L, Wang, P, Hou, H, Chen, C.D, Xu, Y.
Deposit date:2010-05-31
Release date:2010-06-30
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.299 Å)
Cite:Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans
Cell Res., 20, 2010
2YYR
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BU of 2yyr by Molmil
Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide
Descriptor: H3K4Me3 peptide, Pygopus homolog 1, ZINC ION
Authors:Nakamura, Y, Padmanabhan, B, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2007-05-01
Release date:2008-05-06
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide
To be Published
2V87
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BU of 2v87 by Molmil
Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide
Descriptor: HISTONE H3.2, VDJ RECOMBINATION-ACTIVATING PROTEIN 2, ZINC ION
Authors:Ramon-Maiques, S, Yang, W.
Deposit date:2007-08-02
Release date:2007-12-11
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2.
Proc.Natl.Acad.Sci.USA, 104, 2007
2V85
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BU of 2v85 by Molmil
Crystal structure of RAG2-PHD finger in complex with H3R2me1K4me3 peptide
Descriptor: H3R2ME1K4ME3 PEPTIDE, VDJ RECOMBINATION-ACTIVATING PROTEIN 2, ZINC ION
Authors:Ramon-Maiques, S, Yang, W.
Deposit date:2007-08-02
Release date:2007-12-11
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2.
Proc.Natl.Acad.Sci.USA, 104, 2007
2V88
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BU of 2v88 by Molmil
Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide
Descriptor: H3R2ME2SK4ME3 PEPTIDE, VDJ RECOMBINATION-ACTIVATING PROTEIN 2, ZINC ION
Authors:Ramon-Maiques, S, Yang, W.
Deposit date:2007-08-03
Release date:2007-12-11
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2.
Proc.Natl.Acad.Sci.USA, 104, 2007
2V86
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BU of 2v86 by Molmil
Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide
Descriptor: H3R2ME2AK4ME3 PEPTIDE, VDJ RECOMBINATION-ACTIVATING PROTEIN 2, ZINC ION
Authors:Ramon-Maiques, S, Yang, W.
Deposit date:2007-08-02
Release date:2007-12-11
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2.
Proc.Natl.Acad.Sci.USA, 104, 2007
4MZH
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BU of 4mzh by Molmil
Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
Descriptor: MAGNESIUM ION, Peptide from Histone H3.2, Spindlin-1
Authors:Su, X, Ding, X, Li, H.
Deposit date:2013-09-30
Release date:2014-03-26
Last modified:2025-03-26
Method:X-RAY DIFFRACTION (2.204 Å)
Cite:Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1
Genes Dev., 28, 2014
4MZF
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BU of 4mzf by Molmil
Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
Descriptor: CHLORIDE ION, MAGNESIUM ION, Peptide from Histone H3.2, ...
Authors:Su, X, Ding, X, Li, H.
Deposit date:2013-09-30
Release date:2014-03-26
Last modified:2025-03-26
Method:X-RAY DIFFRACTION (2.098 Å)
Cite:Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1
Genes Dev., 28, 2014
2JMJ
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BU of 2jmj by Molmil
NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide
Descriptor: Histone H3, Protein YNG1, ZINC ION
Authors:Ilin, S, Taverna, S.D, Rogers, R.S, Tanny, J.C, Lavender, H, Li, H, Baker, L, Boyle, J, Blair, L.P, Chait, B.T, Patel, D.J, Aitchison, J.D, Tackett, A.J, Allis, C.D.
Deposit date:2006-11-15
Release date:2007-07-03
Last modified:2023-12-20
Method:SOLUTION NMR
Cite:Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs
Mol.Cell, 24, 2006
5Z8L
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BU of 5z8l by Molmil
crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide
Descriptor: Chromatin remodeling protein EBS, H3K27me3 peptide, ZINC ION
Authors:Yang, Z, Du, J.
Deposit date:2018-01-31
Release date:2018-07-25
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (2.005 Å)
Cite:EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.
Nat. Genet., 50, 2018
2JMI
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BU of 2jmi by Molmil
NMR solution structure of PHD finger fragment of Yeast Yng1 protein in free state
Descriptor: Protein YNG1, ZINC ION
Authors:Ilin, S, Taverna, S.D, Rogers, R.S, Tanny, J.C, Lavender, H, Li, H, Baker, L, Boyle, J, Blair, L.P, Chait, B.T, Patel, D.J, Aitchison, J.D, Tackett, A.J, Allis, C.D.
Deposit date:2006-11-15
Release date:2007-07-03
Last modified:2024-10-16
Method:SOLUTION NMR
Cite:Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs
Mol.Cell, 24, 2006
7ZEZ
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BU of 7zez by Molmil
Trimolecular complex Cyp33-RRMdelta alpha : MLL1-PHD3 : H3K4me3
Descriptor: Histone H3, Isoform 3 of Peptidyl-prolyl cis-trans isomerase E, MLL cleavage product N320, ...
Authors:Blatter, M, Allain, F, Meylan, C.
Deposit date:2022-03-31
Release date:2022-04-13
Last modified:2023-05-03
Method:SOLUTION NMR
Cite:RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription.
Sci Adv, 9, 2023
7ZMX
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BU of 7zmx by Molmil
Crystal structure of the Plant Homeodomain (PHD) of human ING3
Descriptor: CALCIUM ION, Inhibitor of growth protein 3, ZINC ION
Authors:Ferreras, M.O, Medrano, F.J, Blanco, F.J.
Deposit date:2022-04-20
Release date:2023-05-10
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Structural analysis of ING3 protein and histone H3 binding.
Int.J.Biol.Macromol., 242, 2023
7BU9
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BU of 7bu9 by Molmil
Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex
Descriptor: H3(K4me3-K9me2) peptide, Spindlin-1
Authors:Zhao, F, Li, H.
Deposit date:2020-04-05
Release date:2020-10-14
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.502 Å)
Cite:Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.
J.Biol.Chem., 295, 2020
4AFL
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BU of 4afl by Molmil
The crystal structure of the ING4 dimerization domain reveals the functional organization of the ING family of chromatin binding proteins.
Descriptor: INHIBITOR OF GROWTH PROTEIN 4
Authors:Culurgioni, S, Munoz, I.G, Moreno, A, Palacios, A, Villate, M, Palmero, I, Montoya, G, Blanco, F.J.
Deposit date:2012-01-19
Release date:2012-02-22
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.275 Å)
Cite:Crystal Structure of Inhibitor of Growth 4 (Ing4) Dimerization Domain Reveals Functional Organization of Ing Family of Chromatin-Binding Proteins.
J.Biol.Chem., 287, 2012
7BQZ
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BU of 7bqz by Molmil
Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide
Descriptor: H3(K4me3-K9me3) peptide, Spindlin-1
Authors:Zhao, F, Li, H.
Deposit date:2020-03-26
Release date:2020-10-14
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.101 Å)
Cite:Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.
J.Biol.Chem., 295, 2020
3KV9
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BU of 3kv9 by Molmil
Structure of KIAA1718 Jumonji domain
Descriptor: FE (II) ION, JmjC domain-containing histone demethylation protein 1D, OXYGEN MOLECULE
Authors:Horton, J.R, Upadhyay, A.K, Qi, H.H, Zhang, X, Shi, Y, Cheng, X.
Deposit date:2009-11-29
Release date:2009-12-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.29 Å)
Cite:Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Nat.Struct.Mol.Biol., 17, 2010
3KVB
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Structure of KIAA1718 Jumonji domain in complex with N-oxalylglycine
Descriptor: JmjC domain-containing histone demethylation protein 1D, N-OXALYLGLYCINE, NICKEL (II) ION, ...
Authors:Horton, J.R, Upadhyay, A.K, Qi, H.H, Zhang, X, Shi, Y, Cheng, X.
Deposit date:2009-11-29
Release date:2009-12-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.69 Å)
Cite:Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Nat.Struct.Mol.Biol., 17, 2010
3KV6
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Structure of KIAA1718, human Jumonji demethylase, in complex with alpha-ketoglutarate
Descriptor: 2-OXOGLUTARIC ACID, FE (II) ION, JmjC domain-containing histone demethylation protein 1D, ...
Authors:Horton, J.R, Upadhyay, A.K, Qi, H.H, Zhang, X, Shi, Y, Cheng, X.
Deposit date:2009-11-29
Release date:2009-12-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Nat.Struct.Mol.Biol., 17, 2010

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