4DBG
 
 | | Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative | | Descriptor: | RING finger protein 31, RanBP-type and C3HC4-type zinc finger-containing protein 1 | | Authors: | Yagi, H, Hiromoto, T, Mizushima, T, Kurimoto, E, Kato, K. | | Deposit date: | 2012-01-15 | | Release date: | 2012-04-04 | | Last modified: | 2024-10-09 | | 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
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2E5U
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2E5Y
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2E5T
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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,ATP synthase epsilon chain, chloroplastic | | 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: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Biochem.J., 425, 2010
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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: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Biochem.J., 425, 2010
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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 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional protein fold determination from backbone amide pseudocontact shifts generated by lanthanide tags at multiple sites
Structure, 21, 2013
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4Y1S
 | | Structural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes | | Descriptor: | CALCIUM ION, Perforin-1 | | Authors: | Conroy, P.J, Yagi, H, Whisstock, J.C, Norton, R.S. | | Deposit date: | 2015-02-09 | | Release date: | 2015-09-02 | | Last modified: | 2024-11-06 | | 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
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4Y1T
 | | Structural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes | | Descriptor: | CALCIUM ION, Perforin-1 | | Authors: | Conroy, P.J, Yagi, H, Whisstock, J.C, Norton, R.S. | | Deposit date: | 2015-02-09 | | Release date: | 2015-09-02 | | Last modified: | 2024-10-30 | | 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
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7XRZ
 | | Crystal structure of BRIL and SRP2070_Fab complex | | Descriptor: | IGG HEAVY CHAIN, IGG LIGHT CHAIN, Soluble cytochrome b562 | | Authors: | Suzuki, M, Miyagi, H, Yasunaga, M, Asada, H, Iwata, S, Saito, J. | | Deposit date: | 2022-05-12 | | Release date: | 2023-05-10 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone.
Acta Crystallogr D Struct Biol, 79, 2023
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7C6A
 | | Crystal structure of AT2R-BRIL and SRP2070_Fab complex | | Descriptor: | IgG Light Chain, IgG heavy chain, SAR1, ... | | Authors: | Suzuki, M, Miyagi, H, Asada, H, Yasunaga, M, Suno, C, Takahashi, Y, Saito, J, Iwata, S. | | Deposit date: | 2020-05-21 | | Release date: | 2020-07-29 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | The discovery of a new antibody for BRIL-fused GPCR structure determination.
Sci Rep, 10, 2020
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7C61
 | | Crystal structure of 5-HT1B-BRIL and SRP2070_Fab complex | | Descriptor: | 5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1B, Ergotamine, IGG HEAVY CHAIN, ... | | Authors: | Suzuki, M, Miyagi, H, Asada, H, Yasunaga, M, Suno, C, Takahashi, Y, Saito, J, Iwata, S. | | Deposit date: | 2020-05-21 | | Release date: | 2020-07-29 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | The discovery of a new antibody for BRIL-fused GPCR structure determination.
Sci Rep, 10, 2020
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8ZUH
 | | Crystal structure of bovine Fbs2/Skp1/Man3GlcNAc2 complex | | Descriptor: | F-box only protein 6, S-phase kinase-associated protein 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: | Satoh, T, Mizushima, T, Yagi, H, Kato, R, Kato, K. | | Deposit date: | 2024-06-09 | | Release date: | 2024-09-04 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structural basis of sugar recognition by SCF FBS2 ubiquitin ligase involved in NGLY1 deficiency.
Febs Lett., 598, 2024
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3WHJ
 | | Crystal structure of Nas2 N-terminal domain | | Descriptor: | CADMIUM ION, Probable 26S proteasome regulatory subunit p27, SULFATE 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: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WHK
 | | Crystal structure of PAN-Rpt5C chimera | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | | 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: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WHL
 | | Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Probable 26S proteasome regulatory subunit p27, Proteasome-activating nucleotidase, ... | | 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: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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5BW7
 | | Crystal structure of nonfucosylated Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | 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: | 2024-11-06 | | 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
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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: | (9S,10R)-9-HYDROXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE, 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3', 5'-D(*CP*GP*GP*TP*CP*AP*CP*GP*AP*GP*G)-3' | | 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: | 2024-05-22 | | 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
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6KRU
 | | Crystal structure of mouse IgG2b Fc | | Descriptor: | Ig gamma-2B chain C region, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Taniguchi, Y, Satoh, T, Yagi, H, Kato, K. | | Deposit date: | 2019-08-22 | | Release date: | 2020-01-22 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Int J Mol Sci, 21, 2019
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6KRV
 | | Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Ig gamma-2B chain C region, ... | | Authors: | Taniguchi, Y, Satoh, T, Yagi, H, Kato, K. | | Deposit date: | 2019-08-22 | | Release date: | 2020-01-22 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Int J Mol Sci, 21, 2019
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2IBK
 | | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, 1,2-ETHANEDIOL, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*AP*T)-3', ... | | 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: | 2023-08-30 | | 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
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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: | (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL, 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') | | 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: | 2024-05-29 | | 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
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2IA6
 | | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, 1,2-ETHANEDIOL, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-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: | 2023-08-30 | | 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
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1DXA
 | | BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3') | | 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: | 2024-03-13 | | 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
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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: | 2024-05-08 | | 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
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