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1WDA
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BU of 1wda by Molmil
Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide
Descriptor: CALCIUM ION, N-[(E)-2-AMINO-1-(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)-2-HYDROXYVINYL]BENZAMIDE, Protein-arginine deiminase type IV, ...
Authors:Arita, K, Hashimoto, H, Shimizu, T, Nakashima, K, Yamada, M, Sato, M.
Deposit date:2004-05-12
Release date:2004-07-13
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural basis for Ca(2+)-induced activation of human PAD4
Nat.Struct.Mol.Biol., 11, 2004
1WD9
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BU of 1wd9 by Molmil
Calcium bound form of human peptidylarginine deiminase type4 (PAD4)
Descriptor: CALCIUM ION, Protein-arginine deiminase type IV, SULFATE ION
Authors:Arita, K, Hashimoto, H, Shimizu, T, Nakashima, K, Yamada, M, Sato, M.
Deposit date:2004-05-12
Release date:2004-07-13
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural basis for Ca(2+)-induced activation of human PAD4
Nat.Struct.Mol.Biol., 11, 2004
1WD8
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BU of 1wd8 by Molmil
Calcium free form of human peptidylarginine deiminase type4 (PAD4)
Descriptor: Protein-arginine deiminase type IV
Authors:Arita, K, Hashimoto, H, Shimizu, T, Nakashima, K, Yamada, M, Sato, M.
Deposit date:2004-05-12
Release date:2004-07-13
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural basis for Ca(2+)-induced activation of human PAD4
Nat.Struct.Mol.Biol., 11, 2004
2E1N
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BU of 2e1n by Molmil
Crystal structure of the Cyanobacterium circadian clock modifier Pex
Descriptor: Pex, SULFATE ION
Authors:Arita, K, Shimizu, T.
Deposit date:2006-10-26
Release date:2006-11-28
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural and Biochemical Characterization of a Cyanobacterium Circadian Clock-modifier Protein
J.Biol.Chem., 282, 2007
2DEX
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BU of 2dex by Molmil
Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17
Descriptor: 10-mer peptide from histone H3, CALCIUM ION, Protein-arginine deiminase type IV, ...
Authors:Arita, K, Shimizu, T, Hashimoto, H, Hidaka, Y, Yamada, M, Sato, M.
Deposit date:2006-02-18
Release date:2006-04-11
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4
Proc.Natl.Acad.Sci.Usa, 103, 2006
2DEW
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BU of 2dew by Molmil
Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8
Descriptor: 10-mer peptide from histone H3, CALCIUM ION, Protein-arginine deiminase type IV, ...
Authors:Arita, K, Shimizu, T, Hashimoto, H, Hidaka, Y, Yamada, M, Sato, M.
Deposit date:2006-02-18
Release date:2006-04-11
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4
Proc.Natl.Acad.Sci.Usa, 103, 2006
2DEY
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BU of 2dey by Molmil
Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3
Descriptor: 10-mer peptide from histone H4, CALCIUM ION, Protein-arginine deiminase type IV, ...
Authors:Arita, K, Shimizu, T, Hashimoto, H, Hidaka, Y, Yamada, M, Sato, M.
Deposit date:2006-02-18
Release date:2006-04-11
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4
Proc.Natl.Acad.Sci.Usa, 103, 2006
3ASK
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BU of 3ask by Molmil
Structure of UHRF1 in complex with histone tail
Descriptor: E3 ubiquitin-protein ligase UHRF1, Histone H3.3, ZINC ION
Authors:Arita, K, Sugita, K, Unoki, M, Hamamoto, R, Sekiyama, N, Tochio, H, Ariyoshi, M, Shirakawa, M.
Deposit date:2010-12-16
Release date:2012-01-25
Last modified:2013-06-05
Method:X-RAY DIFFRACTION (2.904 Å)
Cite:Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1
Proc.Natl.Acad.Sci.USA, 109, 2012
3ASL
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BU of 3asl by Molmil
Structure of UHRF1 in complex with histone tail
Descriptor: 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase UHRF1, Histone H3.3, ...
Authors:Arita, K, Sugita, K, Unoki, M, Hamamoto, R, Sekiyama, N, Tochio, H, Ariyoshi, M, Shirakawa, M.
Deposit date:2010-12-16
Release date:2012-01-25
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.41 Å)
Cite:Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1
Proc.Natl.Acad.Sci.USA, 109, 2012
2ZKG
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BU of 2zkg by Molmil
Crystal structure of unliganded SRA domain of mouse Np95
Descriptor: 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase UHRF1
Authors:Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M.
Deposit date:2008-03-19
Release date:2008-09-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Nature, 455, 2008
2ZKF
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BU of 2zkf by Molmil
Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Descriptor: DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)-3'), DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)-3'), E3 ubiquitin-protein ligase UHRF1
Authors:Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M.
Deposit date:2008-03-19
Release date:2008-09-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Nature, 455, 2008
2ZKD
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BU of 2zkd by Molmil
Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Descriptor: 1,2-ETHANEDIOL, ACETATE ION, DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3'), ...
Authors:Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M.
Deposit date:2008-03-19
Release date:2008-09-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Nature, 455, 2008
2ZKE
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BU of 2zke by Molmil
Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Descriptor: DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3'), E3 ubiquitin-protein ligase UHRF1
Authors:Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M.
Deposit date:2008-03-19
Release date:2008-09-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Nature, 455, 2008
2CVD
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BU of 2cvd by Molmil
Crystal structure analysis of human hematopoietic prostaglandin D synthase complexed with HQL-79
Descriptor: 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE, GLUTATHIONE, GLYCEROL, ...
Authors:Aritake, K, Kado, Y, Inoue, T, Miyano, M, Urade, Y.
Deposit date:2005-06-02
Release date:2006-04-18
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Structural and Functional Characterization of HQL-79, an Orally Selective Inhibitor of Human Hematopoietic Prostaglandin D Synthase.
J.Biol.Chem., 281, 2006
6IIW
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BU of 6iiw by Molmil
Crystal structure of human UHRF1 PHD finger in complex with PAF15
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, E3 ubiquitin-protein ligase UHRF1, PCNA-associated factor, ...
Authors:Arita, K, Kori, S.
Deposit date:2018-10-07
Release date:2019-10-09
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.699 Å)
Cite:Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation.
Nat Commun, 11, 2020
5WVO
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BU of 5wvo by Molmil
Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3
Descriptor: DNA (cytosine-5)-methyltransferase 1, Histone H3.1, Ubiquitin, ...
Authors:Ishiyama, S, Nishiyama, A, Nakanishi, M, Arita, K.
Deposit date:2016-12-28
Release date:2017-11-15
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.997 Å)
Cite:Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance
Mol. Cell, 68, 2017
2RRU
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BU of 2rru by Molmil
Solution structure of the UBA omain of p62 and its interaction with ubiquitin
Descriptor: Sequestosome-1
Authors:Isogai, S, Morimoto, D, Arita, K, Unzai, S, Tenno, T, Hasegawa, J, Sou, Y, Komatsu, M, Tanaka, K, Shirakawa, M, Tochio, H.
Deposit date:2011-06-09
Release date:2011-06-29
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:Crystal structure of the UBA omain of p62 and its interaction with ubiquitin
To be Published
8WMS
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BU of 8wms by Molmil
Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain
Descriptor: Developmental pluripotency-associated protein 3, E3 ubiquitin-protein ligase UHRF1, ZINC ION
Authors:Shiraishi, N, Arita, K.
Deposit date:2023-10-04
Release date:2024-07-31
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain
To Be Published
8YV8
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BU of 8yv8 by Molmil
Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence.
Descriptor: Cell division cycle-associated protein 7, DNA (132-MER), Histone H2A type 1-B/E, ...
Authors:Kikuchi, A, Shikimachi, R, Nishiyama, A, Funabiki, H, Arita, K.
Deposit date:2024-03-28
Release date:2024-07-31
Method:ELECTRON MICROSCOPY (3 Å)
Cite:CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS
To Be Published
7FB7
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BU of 7fb7 by Molmil
Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 5-amino-2,4-dimethylpyridine, DIMETHYL SULFOXIDE, ...
Authors:Kori, S, Arita, K, Yoshimi, S.
Deposit date:2021-07-08
Release date:2022-01-05
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.
Bioorg.Med.Chem., 52, 2021
7XGA
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BU of 7xga by Molmil
NMR strucutre of chimeric protein for model of PHD-Stella complex
Descriptor: Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3, ZINC ION
Authors:Kobayashi, N, Konuma, T, Arita, K.
Deposit date:2022-04-04
Release date:2022-12-07
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.
Nucleic Acids Res., 50, 2022
5YYA
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BU of 5yya by Molmil
Crystal structure of Tandem Tudor Domain of human UHRF1
Descriptor: 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase UHRF1, SULFATE ION
Authors:Kori, S, Defossez, P.A, Arita, K.
Deposit date:2017-12-08
Release date:2018-12-12
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Structure, 27, 2019
5YY9
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BU of 5yy9 by Molmil
Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3
Descriptor: E3 ubiquitin-protein ligase UHRF1, Ligase 1
Authors:Kori, S, Defossez, P.A, Arita, K.
Deposit date:2017-12-08
Release date:2018-12-12
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.653 Å)
Cite:Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Structure, 27, 2019
3WO2
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BU of 3wo2 by Molmil
Crystal structure of human interleukin-18
Descriptor: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE, Interleukin-18, SULFATE ION
Authors:Tsutsumi, N, Kimura, T, Arita, K, Ariyoshi, M, Ohnishi, H, Kondo, N, Shirakawa, M, Kato, Z, Tochio, H.
Deposit date:2013-12-19
Release date:2014-12-17
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:The structural basis for receptor recognition of human interleukin-18
Nat Commun, 5, 2014
3WO4
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BU of 3wo4 by Molmil
Crystal structure of the IL-18 signaling ternary complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Tsutsumi, N, Kimura, T, Arita, K, Ariyoshi, M, Ohnishi, H, Kondo, N, Shirakawa, M, Kato, Z, Tochio, H.
Deposit date:2013-12-19
Release date:2014-12-17
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:The structural basis for receptor recognition of human interleukin-18
Nat Commun, 5, 2014

 

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