Author results

4DBG
  • Download 4dbg
  • View 4dbg
Molmil generated image of 4dbg
CRYSTAL STRUCTURE OF HOIL-1L-UBL COMPLEXED WITH A HOIP-UBA DERIVATIVE
Descriptor:RanBP-type and C3HC4-type zinc finger-containing protein 1, RING finger protein 31
Authors:Yagi, H., Hiromoto, T., Mizushima, T., Kurimoto, E., Kato, K.
Deposit date:2012-01-15
Release date:2012-04-04
Last modified:2012-05-16
Method:X-RAY DIFFRACTION (2.71 Å)
Cite:A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex
Embo Rep., 13, 2012
2E5T
  • Download 2e5t
  • View 2e5t
Molmil generated image of 2e5t
C-TERMINAL DOMAIN OF EPSILON SUBUNIT OF F1F0-ATP SYNTHASE FROM THE THERMOPHILIC BACILLUS PS3 IN THE PRESENCE OF ATP CONDITION
Descriptor:ATP synthase epsilon chain
Authors:Yagi, H., Akutsu, H.
Deposit date:2006-12-22
Release date:2007-07-10
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Structures of the thermophilic F1-ATPase {varepsilon} subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1
Proc.Natl.Acad.Sci.Usa, 104, 2007
2E5U
  • Download 2e5u
  • View 2e5u
Molmil generated image of 2e5u
C-TERMINAL DOMAIN OF EPSILON SUBUNIT OF F1F0-ATP SYNTHASE FROM THE THERMOPHILIC BACILLUS PS3
Descriptor:ATP synthase epsilon chain
Authors:Yagi, H., Akutsu, H.
Deposit date:2006-12-25
Release date:2007-07-10
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Structures of the thermophilic F1-ATPase {varepsilon} subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1
Proc.Natl.Acad.Sci.Usa, 104, 2007
2E5Y
  • Download 2e5y
  • View 2e5y
Molmil generated image of 2e5y
EPSILON SUBUNIT AND ATP COMPLEX OF F1F0-ATP SYNTHASE FROM THE THERMOPHILIC BACILLUS PS3
Descriptor:ATP synthase epsilon chain, ADENOSINE-5'-TRIPHOSPHATE
Authors:Yagi, H., Akutsu, H.
Deposit date:2006-12-25
Release date:2007-07-10
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Structures of the thermophilic F1-ATPase {varepsilon} subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1
Proc.Natl.Acad.Sci.Usa, 104, 2007
2RQ6
  • Download 2rq6
  • View 2rq6
Molmil generated image of 2rq6
SOLUTION STRUCTURE OF THE EPSILON SUBUNIT OF THE F1-ATPASE FROM THERMOSYNECHOCOCCUS ELONGATUS BP-1
Descriptor:ATP synthase epsilon chain
Authors:Yagi, H., Konno, H., Murakami-Fuse, T., Oroguchi, H., Akutsu, T., Ikeguchi, M., Hisabori, T.
Deposit date:2009-03-03
Release date:2010-01-12
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Biochem.J., 425, 2010
2RQ7
  • Download 2rq7
  • View 2rq7
Molmil generated image of 2rq7
SOLUTION STRUCTURE OF THE EPSILON SUBUNIT CHIMERA COMBINING THE N-TERMINAL BETA-SANDWICH DOMAIN FROM T. ELONGATUS BP-1 F1 AND THE C-TERMINAL ALPHA-HELICAL DOMAIN FROM SPINACH CHLOROPLAST F1
Descriptor:ATP synthase epsilon chain
Authors:Yagi, H., Konno, H., Murakami-Fuse, T., Oroguchi, H., Akutsu, T., Ikeguchi, M., Hisabori, T.
Deposit date:2009-03-03
Release date:2010-01-12
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Biochem.J., 425, 2010
2M66
  • Download 2m66
  • View 2m66
Molmil generated image of 2m66
ENDOPLASMIC RETICULUM PROTEIN 29 (ERP29) C-TERMINAL DOMAIN: 3D PROTEIN FOLD DETERMINATION FROM BACKBONE AMIDE PSEUDOCONTACT SHIFTS GENERATED BY LANTHANIDE TAGS AT MULTIPLE SITES
Descriptor:Endoplasmic reticulum resident protein 29
Authors:Yagi, H., Pilla, K., Maleckis, A., Graham, B., Huber, T., Otting, G.
Deposit date:2013-03-26
Release date:2013-07-10
Method:SOLUTION NMR
Cite:Three-dimensional protein fold determination from backbone amide pseudocontact shifts generated by lanthanide tags at multiple sites
Structure, 21, 2013
4Y1S
  • Download 4y1s
  • View 4y1s
Molmil generated image of 4y1s
STRUCTURAL BASIS FOR CA2+-MEDIATED INTERACTION OF THE PERFORIN C2 DOMAIN WITH LIPID MEMBRANES
Descriptor:Perforin-1, CALCIUM ION
Authors:Conroy, P.J., Yagi, H., Whisstock, J.C., Norton, R.S.
Deposit date:2015-02-09
Release date:2015-09-02
Last modified:2017-12-13
Method:X-RAY DIFFRACTION (1.611 Å)
Cite:Structural Basis for Ca2+-mediated Interaction of the Perforin C2 Domain with Lipid Membranes.
J.Biol.Chem., 290, 2015
4Y1T
  • Download 4y1t
  • View 4y1t
Molmil generated image of 4y1t
STRUCTURAL BASIS FOR CA2+-MEDIATED INTERACTION OF THE PERFORIN C2 DOMAIN WITH LIPID MEMBRANES
Descriptor:Perforin-1, CALCIUM ION
Authors:Conroy, P.J., Yagi, H., Whisstock, J.C., Norton, R.S.
Deposit date:2015-02-09
Release date:2015-09-02
Last modified:2015-10-28
Method:X-RAY DIFFRACTION (2.666 Å)
Cite:Structural Basis for Ca2+-mediated Interaction of the Perforin C2 Domain with Lipid Membranes.
J.Biol.Chem., 290, 2015
3WHJ
  • Download 3whj
  • View 3whj
Molmil generated image of 3whj
CRYSTAL STRUCTURE OF NAS2 N-TERMINAL DOMAIN
Descriptor:Probable 26S proteasome regulatory subunit p27, SULFATE ION, CADMIUM ION
Authors:Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.
Deposit date:2013-08-26
Release date:2014-03-26
Last modified:2014-04-16
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structural Basis for Proteasome Formation Controlled by an Assembly Chaperone Nas2
Structure, 2014
3WHK
  • Download 3whk
  • View 3whk
Molmil generated image of 3whk
CRYSTAL STRUCTURE OF PAN-RPT5C CHIMERA
Descriptor:Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A, ADENOSINE-5'-TRIPHOSPHATE
Authors:Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.
Deposit date:2013-08-26
Release date:2014-03-26
Last modified:2017-08-16
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural Basis for Proteasome Formation Controlled by an Assembly Chaperone Nas2
Structure, 2014
3WHL
  • Download 3whl
  • View 3whl
Molmil generated image of 3whl
CRYSTAL STRUCTURE OF NAS2 N-TERMINAL DOMAIN COMPLEXED WITH PAN-RPT5C CHIMERA
Descriptor:Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A, Probable 26S proteasome regulatory subunit p27, ...
Authors:Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.
Deposit date:2013-08-26
Release date:2014-03-26
Last modified:2017-08-16
Method:X-RAY DIFFRACTION (4 Å)
Cite:Structural Basis for Proteasome Formation Controlled by an Assembly Chaperone Nas2
Structure, 2014
2IA6
  • Download 2ia6
  • View 2ia6
Molmil generated image of 2ia6
BYPASS OF MAJOR BENZOPYRENE-DG ADDUCT BY Y-FAMILY DNA POLYMERASE WITH UNIQUE STRUCTURAL GAP
Descriptor:DNA polymerase IV, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-3', 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', ...
Authors:Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.
Deposit date:2006-09-07
Release date:2007-09-11
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.
Proc.Natl.Acad.Sci.Usa, 104, 2007
2IBK
  • Download 2ibk
  • View 2ibk
Molmil generated image of 2ibk
BYPASS OF MAJOR BENZOPYRENE-DG ADDUCT BY Y-FAMILY DNA POLYMERASE WITH UNIQUE STRUCTURAL GAP
Descriptor:5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*AP*T)-3', 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', DNA polymerase IV, ...
Authors:Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.
Deposit date:2006-09-11
Release date:2007-09-11
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.
Proc.Natl.Acad.Sci.Usa, 104, 2007
2ROU
  • Download 2rou
  • View 2rou
Molmil generated image of 2rou
STEREOSPECIFIC CONFORMATIONS OF N2-DG 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE DNA ADDUCTS: 3'-INTERCALATION OF THE 1R ADDUCT AND 5'-MINOR GROOVE ORIENTATION OF THE 1S ADDUCT IN AN ITERATED (CG)3 REPEAT
Descriptor:DNA (5'-D(*DAP*DTP*DCP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DAP*DTP*DG)-3'), DNA (5'-D(*DCP*DAP*DTP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DGP*DAP*DT)-3'), (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL
Authors:Wang, Y., Kroth, H., Yagi, H., Sayer, J.M., Kumar, S., Jerina, D.M., Stone, M.P.
Deposit date:2008-04-20
Release date:2009-03-03
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:3'-Intercalation of a N2-dG 1R-trans-anti-benzo[c]phenanthrene DNA adduct in an iterated (CG)3 repeat
Chem.Res.Toxicol., 21, 2008
1DXA
  • Download 1dxa
  • View 1dxa
Molmil generated image of 1dxa
BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA
Descriptor:DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3'), DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'), 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
Authors:Yeh, H.J.C., Sayer, J.M., Liu, X., Altieri, A.S., Byrd, R.A., Lakshman, M.K., Yagi, H., Schurter, E.J., Gorenstein, D.G., Jerina, D.M.
Deposit date:1995-09-01
Release date:1995-12-07
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA
Biochemistry, 34, 1995
1N8C
  • Download 1n8c
  • View 1n8c
Molmil generated image of 1n8c
SOLUTION STRUCTURE OF A CIS-OPENED (10R)-N6-DEOXYADENOSINE ADDUCT OF (9S,10R)-(9,10)-EPOXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE IN A DNA DUPLEX
Descriptor:5'-D(*CP*GP*GP*TP*CP*AP*CP*GP*AP*GP*G)-3', 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3', (9S,10R)-9-HYDROXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE
Authors:Volk, D.E., Thiviyanathan, V., Rice, J.S., Luxon, B.A., Shah, J.H., Yagi, H., Sayer, J.M., Yeh, H.J.C., Jerina, D.M., Gorenstein, D.G.
Deposit date:2002-11-20
Release date:2003-02-14
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex
Biochemistry, 42, 2003
1WDI
  • Download 1wdi
  • View 1wdi
Molmil generated image of 1wdi
CRYSTAL STRUCTURE OF TT0907 FROM THERMUS THERMOPHILUS HB8
Descriptor:hypothetical protein TT0907, CITRIC ACID
Authors:Idaka, M., Yagi, H., Murayama, K., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-05-17
Release date:2004-11-17
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal Structure Of TT0907 From Thermus Thermophilus HB8
To be published
2JZ4
  • Download 2jz4
  • View 2jz4
Molmil generated image of 2jz4
PUTATIVE 32 KDA MYROSINASE BINDING PROTEIN AT3G16450.1 FROM ARABIDOPSIS THALIANA
Descriptor:Jasmonate inducible protein isolog
Authors:Takeda, N., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A.M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Guntert, P., Aceti, D.J., Markley, J.L., Kainosho, M., Center for Eukaryotic Structural Genomics (CESG)
Deposit date:2007-12-28
Release date:2008-02-19
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR.
Febs J., 275, 2008
3AY4
  • Download 3ay4
  • View 3ay4
Molmil generated image of 3ay4
CRYSTAL STRUCTURE OF NONFUCOSYLATED FC COMPLEXED WITH BIS-GLYCOSYLATED SOLUBLE FORM OF FC GAMMA RECEPTOR IIIA
Descriptor:Ig gamma-1 chain C region, Low affinity immunoglobulin gamma Fc region receptor III-A, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Mizushima, T., Takemoto, E., Yagi, H., Shibata-Koyama, M., Isoda, Y., Iida, S., Satoh, M., Kato, K.
Deposit date:2011-04-28
Release date:2011-08-03
Last modified:2011-11-09
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural basis for improved efficacy of therapeutic antibodies on defucosylation of their Fc glycans
Genes Cells, 16, 2011
3VR0
  • Download 3vr0
  • View 3vr0
Molmil generated image of 3vr0
CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS PBAB, AN ARCHAEAL PROTEASOME ACTIVATOR
Descriptor:Putative uncharacterized protein, GOLD ION
Authors:Kumoi, K., Satoh, T., Hiromoto, T., Mizushima, T., Kamiya, Y., Noda, M., Uchiyama, S., Murata, K., Yagi, H., Kato, K.
Deposit date:2012-04-02
Release date:2013-04-03
Last modified:2013-07-31
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:An archaeal homolog of proteasome assembly factor functions as a proteasome activator
Plos One, 8, 2013
5BW7
  • Download 5bw7
  • View 5bw7
Molmil generated image of 5bw7
CRYSTAL STRUCTURE OF NONFUCOSYLATED FC Y296W MUTANT COMPLEXED WITH BIS-GLYCOSYLATED SOLUBLE FORM OF FC GAMMA RECEPTOR IIIA
Descriptor:Ig gamma-1 chain C region, Low affinity immunoglobulin gamma Fc region receptor III-A, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Isoda, Y., Yagi, H., Satoh, T., Shibata-Koyama, M., Masuda, K., Satoh, M., Kato, K., Iida, S.
Deposit date:2015-06-06
Release date:2015-10-14
Last modified:2015-11-11
Method:X-RAY DIFFRACTION (3 Å)
Cite:Importance of the Side Chain at Position 296 of Antibody Fc in Interactions with Fc gamma RIIIa and Other Fc gamma Receptors
Plos One, 10, 2015
5XJE
  • Download 5xje
  • View 5xje
Molmil generated image of 5xje
CRYSTAL STRUCTURE OF FUCOSYLATED IGG1 FC COMPLEXED WITH BIS-GLYCOSYLATED SOLUBLE FORM OF FC GAMMA RECEPTOR IIIA
Descriptor:Immunoglobulin gamma-1 heavy chain, Low affinity immunoglobulin gamma Fc region receptor III-A, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Sakae, Y., Satoh, T., Yagi, H., Yanaka, S., Yamaguchi, T., Isoda, Y., Iida, S., Okamoto, Y., Kato, K.
Deposit date:2017-05-01
Release date:2017-11-01
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
5XJF
  • Download 5xjf
  • View 5xjf
Molmil generated image of 5xjf
CRYSTAL STRUCTURE OF FUCOSYLATED IGG FC Y296W MUTANT COMPLEXED WITH BIS-GLYCOSYLATED SOLUBLE FORM OF FC GAMMA RECEPTOR IIIA
Descriptor:Immunoglobulin gamma-1 heavy chain, Low affinity immunoglobulin gamma Fc region receptor III-A, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Sakae, Y., Satoh, T., Yagi, H., Yanaka, S., Yamaguchi, T., Isoda, Y., Iida, S., Okamoto, Y., Kato, K.
Deposit date:2017-05-01
Release date:2017-11-01
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
5Y9N
  • Download 5y9n
  • View 5y9n
Molmil generated image of 5y9n
CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS PBAA (MONOCLINIC FORM), AN ARCHAEAL HOMOLOG OF PROTEASOME-ASSEMBLY CHAPERONE
Descriptor:PbaA, CHLORIDE ION
Authors:Yagi-Utsumi, M., Sikdar, A., Kozai, T., Inoue, R., Sugiyama, M., Uchihashi, T., Satoh, T., Kato, K.
Deposit date:2017-08-26
Release date:2018-01-17
Last modified:2018-02-14
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation
Protein Eng. Des. Sel., 31, 2018
<12>