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5GVI
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BU of 5gvi by Molmil
Zebrafish USP30 in complex with Lys6-linked diubiquitin
Descriptor: Ubiquitin carboxyl-terminal hydrolase 30, ZINC ION, ubiquitin
Authors:Sato, Y, Fukai, S.
Deposit date:2016-09-05
Release date:2017-09-13
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30
Nat. Struct. Mol. Biol., 24, 2017
3WWQ
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BU of 3wwq by Molmil
Crystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin
Descriptor: Fanconi anemia-associated protein of 20 kDa, Ubiquitin, ZINC ION
Authors:Sato, Y, Fukai, S.
Deposit date:2014-06-23
Release date:2015-05-13
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural Basis for Ubiquitin Recognition by Ubiquitin-Binding Zinc Finger of FAAP20
Plos One, 10, 2015
3VON
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BU of 3von by Molmil
Crystalstructure of the ubiquitin protease
Descriptor: Ubiquitin thioesterase OTUB1, Ubiquitin-conjugating enzyme E2 N, Ubiquitin-conjugating enzyme E2 variant 2
Authors:Sato, Y, Fukai, S.
Deposit date:2012-01-30
Release date:2012-05-30
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.15 Å)
Cite:Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13.
J.Biol.Chem., 287, 2012
3VLC
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BU of 3vlc by Molmil
Crystal structure of S. cerevisiae Get3 in the semi open conformation in complex with Get1 cytosolic domain at 4.5 angstrom resolution
Descriptor: ADENOSINE-5'-DIPHOSPHATE, ATPase GET3, Golgi to ER traffic protein 1
Authors:Kubota, K, Yamagata, A, Fukai, S.
Deposit date:2011-11-30
Release date:2012-06-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (4.5 Å)
Cite:Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces
J.Mol.Biol., 422, 2012
4YH7
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BU of 4yh7 by Molmil
Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein-like 1, ...
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-27
Release date:2015-05-06
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (4.4 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YFE
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BU of 4yfe by Molmil
Crystal structure of PTP delta Fn1-Fn2
Descriptor: Receptor-type tyrosine-protein phosphatase delta
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-25
Release date:2015-05-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.972 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YFG
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BU of 4yfg by Molmil
Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor-type tyrosine-protein phosphatase delta
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-25
Release date:2015-05-06
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (3.491 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YH6
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BU of 4yh6 by Molmil
Crystal structure of IL1RAPL1 ectodomain
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein-like 1, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-27
Release date:2015-05-06
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (3 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YVH
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BU of 4yvh by Molmil
Crystal Structure of H. influenzae TrmD in complex with sinefungin
Descriptor: SINEFUNGIN, tRNA (guanine-N(1)-)-methyltransferase
Authors:Yoshida, K, Ito, T, Yokoyama, S.
Deposit date:2015-03-20
Release date:2015-07-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
4YFD
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BU of 4yfd by Molmil
Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein, Receptor-type tyrosine-protein phosphatase delta
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-25
Release date:2015-05-06
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (3.253 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YVG
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BU of 4yvg by Molmil
Crystal Structure of H. influenzae TrmD in complex with AdoMet
Descriptor: S-ADENOSYLMETHIONINE, tRNA (guanine-N(1)-)-methyltransferase
Authors:Ito, T, Yokoyama, S.
Deposit date:2015-03-20
Release date:2015-07-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.549 Å)
Cite:Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
4YVK
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BU of 4yvk by Molmil
Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C)
Descriptor: SINEFUNGIN, tRNA, tRNA (guanine-N(1)-)-methyltransferase
Authors:Yoshida, K, Ito, T, Yokoyama, S.
Deposit date:2015-03-20
Release date:2015-07-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.002 Å)
Cite:Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
4YVJ
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BU of 4yvj by Molmil
Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36U)
Descriptor: SINEFUNGIN, tRNA, tRNA (guanine-N(1)-)-methyltransferase
Authors:Yoshida, K, Ito, T, Yokoyama, S.
Deposit date:2015-03-20
Release date:2015-07-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
4YVI
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BU of 4yvi by Molmil
Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA
Descriptor: SINEFUNGIN, tRNA, tRNA (guanine-N(1)-)-methyltransferase
Authors:Yoshida, K, Ito, T, Yokoyama, S.
Deposit date:2015-03-20
Release date:2015-07-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.01 Å)
Cite:Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
3WXE
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BU of 3wxe by Molmil
Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
Descriptor: Ubiquitin, Uncharacterized protein
Authors:Sato, Y, Fukai, S.
Deposit date:2014-07-30
Release date:2015-02-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Nat.Struct.Mol.Biol., 22, 2015
3WXG
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BU of 3wxg by Molmil
Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin
Descriptor: Ubiquitin, Uncharacterized protein
Authors:Sato, Y, Fukai, S.
Deposit date:2014-07-30
Release date:2015-02-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Nat.Struct.Mol.Biol., 22, 2015
3WXF
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BU of 3wxf by Molmil
Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin
Descriptor: SULFATE ION, Ubiquitin, Uncharacterized protein
Authors:Sato, Y, Fukai, S.
Deposit date:2014-07-30
Release date:2015-02-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Nat.Struct.Mol.Biol., 22, 2015
3A4T
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BU of 3a4t by Molmil
Crystal structure of aTrm4 from M.jannaschii with sinefungin
Descriptor: Putative methyltransferase MJ0026, SINEFUNGIN
Authors:Hirano, M, Kuratani, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2009-07-14
Release date:2010-06-30
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
J.Mol.Biol., 401, 2010
3AJD
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BU of 3ajd by Molmil
Crystal structure of ATRM4
Descriptor: GLYCEROL, ISOPROPYL ALCOHOL, Putative methyltransferase MJ0026
Authors:Hirano, M, Kuratani, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2010-06-01
Release date:2010-06-30
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (1.27 Å)
Cite:Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
J.Mol.Biol., 401, 2010
3B2E
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BU of 3b2e by Molmil
Crystal structure of S. cerevisiae Get3 in the open conformation in complex with Get1 cytosolic domain
Descriptor: ADENOSINE-5'-DIPHOSPHATE, ATPase GET3, Golgi to ER traffic protein 1
Authors:Kubota, K, Yamagata, A, Fukai, S.
Deposit date:2011-07-30
Release date:2012-06-27
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (3 Å)
Cite:Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces
J.Mol.Biol., 422, 2012
5XIT
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BU of 5xit by Molmil
Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II
Descriptor: E3 ubiquitin-protein ligase RNF168, GLYCEROL, PRASEODYMIUM ION, ...
Authors:Takahashi, T.S, Sato, Y, Fukai, S.
Deposit date:2017-04-27
Release date:2018-03-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Nat Commun, 9, 2018
5XIS
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BU of 5xis by Molmil
Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I
Descriptor: E3 ubiquitin-protein ligase RNF168, MAGNESIUM ION, Ubiquitin-40S ribosomal protein S27a, ...
Authors:Takahashi, T.S, Sato, Y, Fukai, S.
Deposit date:2017-04-27
Release date:2018-03-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Nat Commun, 9, 2018
5XIU
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BU of 5xiu by Molmil
Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin
Descriptor: 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase RNF168, Ubiquitin-40S ribosomal protein S27a
Authors:Takahashi, T.S, Sato, Y, Fukai, S.
Deposit date:2017-04-27
Release date:2018-03-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Nat Commun, 9, 2018
5Y32
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BU of 5y32 by Molmil
Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1
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:Yamagata, A, Fukai, S.
Deposit date:2017-07-27
Release date:2017-08-16
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (2.701 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
5YDK
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BU of 5ydk by Molmil
Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form
Descriptor: E3 ubiquitin-protein ligase RNF168, GLYCEROL, Ubiquitin-40S ribosomal protein S27a
Authors:Takahashi, T.S, Sato, Y, Fukai, S.
Deposit date:2017-09-13
Release date:2018-03-07
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (2.505 Å)
Cite:Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168
Nat Commun, 9, 2018

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