Author results

3VIV
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1510-N MEMBRANE-BOUND STOMATIN-SPECIFIC PROTEASE K138A MUTANT IN COMPLEX WITH A SUBSTRATE PEPTIDE
Descriptor:441aa long hypothetical nfeD protein, PH STOMATIN PH1511, GLYCEROL, ...
Authors:Yokoyama, H., Matsui, I., Fujii, S.
Deposit date:2011-10-12
Release date:2012-05-23
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Crystal structure of a membrane stomatin-specific protease in complex with a substrate Peptide
Biochemistry, 51, 2012
3VW3
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ANTIBODY 64M-5 FAB IN COMPLEX WITH A DOUBLE-STRANDED DNA (6-4) PHOTOPRODUCT
Descriptor:Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3'), ...
Authors:Yokoyama, H., Mizutani, R., Satow, Y.
Deposit date:2012-07-30
Release date:2013-03-27
Last modified:2014-04-30
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab
Acta Crystallogr.,Sect.D, 69, 2013
6IDG
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ANTIBODY 64M-5 FAB IN COMPLEX WITH DT(6-4)T
Descriptor:Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), DNA (5'-D(*(64T)P*(5PY))-3')
Authors:Yokoyama, H., Mizutani, R., Noguchi, S., Hayashida, N.
Deposit date:2018-09-10
Release date:2019-02-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms
Acta Crystallogr.,Sect.F, 75, 2019
6IDH
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ANTIBODY 64M-5 FAB IN LIGAND-FREE FORM
Descriptor:Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)
Authors:Yokoyama, H., Mizutani, R., Noguchi, S., Hayashida, N.
Deposit date:2018-09-10
Release date:2019-02-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms
Acta Crystallogr.,Sect.F, 75, 2019
1KEG
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ANTIBODY 64M-2 FAB COMPLEXED WITH DTT(6-4)TT
Descriptor:5'-D(*TP*(64T)P*TP*T)-3', Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain), Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain), ...
Authors:Yokoyama, H., Mizutani, R., Satow, Y., Sato, K., Komatsu, Y., Ohtsuka, E., Nikaido, O.
Deposit date:2001-11-15
Release date:2002-11-15
Last modified:2012-03-28
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides.
Acta Crystallogr.,Sect.D, 68, 2012
2DEO
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1510-N MEMBRANE PROTEASE SPECIFIC FOR A STOMATIN HOMOLOG FROM PYROCOCCUS HORIKOSHII
Descriptor:441aa long hypothetical nfeD protein
Authors:Yokoyama, H., Matsui, I.
Deposit date:2006-02-16
Release date:2006-05-16
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Molecular Structure of a Novel Membrane Protease Specific for a Stomatin Homolog from the Hyperthermophilic Archaeon Pyrococcus horikoshii
J.Mol.Biol., 358, 2006
3BK6
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CRYSTAL STRUCTURE OF A CORE DOMAIN OF STOMATIN FROM PYROCOCCUS HORIKOSHII
Descriptor:PH stomatin
Authors:Yokoyama, H., Fujii, S., Matsui, I.
Deposit date:2007-12-05
Release date:2008-02-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold
J.Mol.Biol., 376, 2008
3BPP
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1510-N MEMBRANE PROTEASE K138A MUTANT SPECIFIC FOR A STOMATIN HOMOLOG FROM PYROCOCCUS HORIKOSHII
Descriptor:1510-N membrane protease
Authors:Yokoyama, H., Hamamatsu, S., Fujii, S., Matsui, I.
Deposit date:2007-12-19
Release date:2008-04-29
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin
J.SYNCHROTRON RADIAT., 15, 2008
3WG5
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1510-N MEMBRANE-BOUND STOMATIN-SPECIFIC PROTEASE K138A MUTANT IN COMPLEX WITH A SUBSTRATE PEPTIDE UNDER HEAT TREATMENT
Descriptor:441aa long hypothetical nfeD protein, PH1511 stomatin, GLYCEROL, ...
Authors:Yokoyama, H., Fujii, S., Matsui, I.
Deposit date:2013-07-26
Release date:2013-10-23
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease
J.SYNCHROTRON RADIAT., 20, 2013
3WWV
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C-TERMINAL DOMAIN OF STOMATIN OPERON PARTNER PROTEIN 1510-C FROM PYROCOCCUS HORIKOSHII
Descriptor:Stomatin operon partner protein, SODIUM ION
Authors:Yokoyama, H., Matsui, I.
Deposit date:2014-06-30
Release date:2014-10-01
Last modified:2015-01-21
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of the stomatin operon partner protein from Pyrococcus horikoshii indicates the formation of a multimeric assembly
FEBS Open Bio, 4, 2014
4EVB
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CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS39 ZINC SOAKED (20MM)
Descriptor:Neutrophil-activating protein, ZINC ION, 1,2-ETHANEDIOL, ...
Authors:Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.
Deposit date:2012-04-26
Release date:2012-06-27
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form
Biochem.Biophys.Res.Commun., 422, 2012
4EVC
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CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS39 CADMIUM LOADED (COCRYSTALLIZATION 50MM)
Descriptor:Neutrophil-activating protein, CADMIUM ION
Authors:Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.
Deposit date:2012-04-26
Release date:2012-06-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form
Biochem.Biophys.Res.Commun., 422, 2012
4EVD
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CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS29 CADMIUM LOADED (COCRYSTALLIZATION 50MM)
Descriptor:Neutrophil-activating protein, CADMIUM ION
Authors:Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.
Deposit date:2012-04-26
Release date:2012-06-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form
Biochem.Biophys.Res.Commun., 422, 2012
4EVE
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CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS29 IN APO FORM
Descriptor:Neutrophil-activating protein, SULFATE ION
Authors:Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.
Deposit date:2012-04-26
Release date:2012-06-27
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form
Biochem.Biophys.Res.Commun., 422, 2012
1EHL
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64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T
Descriptor:5'-(D(5HT)P*(6-4)T)-3', ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (LIGHT CHAIN), ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (HEAVY CHAIN)
Authors:Yokoyama, H., Mizutani, R., Satow, Y., Komatsu, Y., Ohtsuka, E., Nikaido, O.
Deposit date:2000-02-21
Release date:2001-02-21
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation.
J.Mol.Biol., 299, 2000
3WPN
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KINESIN SPINDLE PROTEIN EG5 IN COMPLEX WITH ATP-COMPETITIVE INHIBITOR PVZB1194
Descriptor:Kinesin-like protein KIF11, 3'-fluoro-4'-(trifluoromethyl)biphenyl-4-sulfonamide
Authors:Yokoyama, H., Katoh, S., Fujii, S.
Deposit date:2014-01-14
Release date:2015-01-21
Last modified:2015-04-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural basis of new allosteric inhibition in Kinesin spindle protein eg5
Acs Chem.Biol., 10, 2015
5ZO7
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KINESIN SPINDLE PROTEIN EG5 IN COMPLEX WITH STLC-TYPE INHIBITOR PVEI0138
Descriptor:Kinesin-like protein KIF11, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ...
Authors:Yokoyama, H., Sato, K.
Deposit date:2018-04-12
Release date:2018-10-10
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors
ACS OMEGA, 2018
5ZO8
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EG5 MOTOR DOMAIN IN COMPLEX WITH STLC-TYPE INHIBITOR PVEI0021 (P21 TYPE)
Descriptor:Kinesin-like protein KIF11, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ...
Authors:Yokoyama, H., Sato, K.
Deposit date:2018-04-12
Release date:2018-10-10
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors
ACS OMEGA, 2018
5ZO9
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EG5 MOTOR DOMAIN IN COMPLEX WITH STLC-TYPE INHIBITOR PVEI0021 (C2 TYPE)
Descriptor:Kinesin-like protein KIF11, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ...
Authors:Yokoyama, H., Sato, K.
Deposit date:2018-04-12
Release date:2018-10-10
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors
ACS OMEGA, 2018
3O59
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DNA POLYMERASE D LARGE SUBUNIT DP2(1-300) FROM PYROCOCCUS HORIKOSHII
Descriptor:DNA polymerase II large subunit
Authors:Yokoyama, H., Shen, Y., Matsui, I.
Deposit date:2010-07-28
Release date:2011-01-05
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii
Febs Lett., 585, 2011
3T9J
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CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS39 IN APO FORM
Descriptor:Neutrophil-activating protein, 1,2-ETHANEDIOL
Authors:Tsuruta, O., Yokoyama, H., Fujii, S.
Deposit date:2011-08-03
Release date:2012-02-08
Last modified:2012-04-25
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP)
Acta Crystallogr.,Sect.F, 68, 2012
3TA8
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CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS39 IRON LOADED (COCRYSTALLIZATION 5MM)
Descriptor:Neutrophil-activating protein, FE (III) ION, 1,2-ETHANEDIOL
Authors:Tsuruta, O., Yokoyama, H., Fujii, S.
Deposit date:2011-08-03
Release date:2012-02-08
Last modified:2012-04-25
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP)
Acta Crystallogr.,Sect.F, 68, 2012
2EXD
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THE SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF A NFED HOMOLOG FROM PYROCOCCUS HORIKOSHII
Descriptor:nfeD short homolog
Authors:Kuwahara, Y., Ohno, A., Morii, T., Tochio, H., Shirakawa, M., Hiroaki, H.
Deposit date:2005-11-08
Release date:2006-12-12
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold.
Protein Sci., 17, 2008
5XPT
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CRYSTAL STRUCTURE OF MAD2L2/REV7 IN COMPLEX WITH A CAMP FRAGMENT IN A TETRAGONAL CRYSTAL
Descriptor:Mitotic spindle assembly checkpoint protein MAD2B, Chromosome alignment-maintaining phosphoprotein 1
Authors:Hara, K., Taharazako, S., Hashimoto, H.
Deposit date:2017-06-05
Release date:2017-09-20
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (2.102 Å)
Cite:Dynamic feature of mitotic arrest deficient 2-like protein 2 (MAD2L2) and structural basis for its interaction with chromosome alignment-maintaining phosphoprotein (CAMP).
J. Biol. Chem., 292, 2017
5XPU
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CRYSTAL STRUCTURE OF MAD2L2/REV7 IN COMPLEX WITH A CAMP FRAGMENT IN A MONOCLINIC CRYSTAL
Descriptor:Mitotic spindle assembly checkpoint protein MAD2B, Chromosome alignment-maintaining phosphoprotein 1
Authors:Hara, K., Taharazako, S., Hashimoto, H.
Deposit date:2017-06-05
Release date:2017-09-20
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (2.304 Å)
Cite:Dynamic feature of mitotic arrest deficient 2-like protein 2 (MAD2L2) and structural basis for its interaction with chromosome alignment-maintaining phosphoprotein (CAMP).
J. Biol. Chem., 292, 2017
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