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2RRC
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BU of 2rrc by Molmil
Solution Structure of RNA aptamer against AML1 Runt domain
Descriptor: 5'-R(P*GP*GP*AP*CP*CP*CP*(AP7)P*CP*CP*AP*CP*GP*GP*CP*GP*AP*GP*GP*UP*CP*CP*A)-3'
Authors:Nomura, Y, Fujiwara, K, Chiba, M, Fukunaga, J, Tanaka, Y, Iibuchi, H, Tanaka, T, Nakamura, Y, Kawai, G, Kozu, T, Sakamoto, T.
Deposit date:2010-06-23
Release date:2011-06-29
Last modified:2020-02-26
Method:SOLUTION NMR
Cite:A novel high affinity RNA motif that mimics DNA in AML1 Runt domain binding
To be Published
2FDT
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BU of 2fdt by Molmil
Solution structure of a conserved RNA hairpin of eel LINE UnaL2
Descriptor: 36-mer
Authors:Nomura, Y, Baba, S, Nakazato, S, Sakamoto, T, Kajikawa, M, Okada, N, Kawai, G.
Deposit date:2005-12-14
Release date:2006-12-05
Last modified:2022-03-09
Method:SOLUTION NMR
Cite:Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
Nucleic Acids Res., 34, 2006
6D31
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BU of 6d31 by Molmil
Structure of human Usb1 with adenosine 5'-monophosphate
Descriptor: ADENOSINE MONOPHOSPHATE, CHLORIDE ION, GLYCEROL, ...
Authors:Nomura, Y, Montemayor, E.J, Butcher, S.E.
Deposit date:2018-04-14
Release date:2018-09-05
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.
Nucleic Acids Res., 46, 2018
6D2Z
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BU of 6d2z by Molmil
Structure of human Usb1 with uridine-adenosine, inactive H208Q mutant
Descriptor: 5'-R(UP*A)-3'), CHLORIDE ION, U6 snRNA phosphodiesterase
Authors:Nomura, Y, Montemayor, E.J, Butcher, S.E.
Deposit date:2018-04-14
Release date:2018-09-05
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.18 Å)
Cite:Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.
Nucleic Acids Res., 46, 2018
6D30
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BU of 6d30 by Molmil
Structure of human Usb1 with uridine-uridine, inactive H208Q mutant
Descriptor: CHLORIDE ION, RNA (5'-R(UP*U)-3'), U6 snRNA phosphodiesterase
Authors:Nomura, Y, Montemayor, E.J, Butcher, S.E.
Deposit date:2018-04-14
Release date:2018-09-05
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.17 Å)
Cite:Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.
Nucleic Acids Res., 46, 2018
3AGV
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BU of 3agv by Molmil
Crystal structure of a human IgG-aptamer complex
Descriptor: 5'-R(*GP*GP*AP*GP*GP*(UFT)P*GP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*GP*AP*AP*A*GP*GP*AP*AP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*A)-3', CALCIUM ION, Ig gamma-1 chain C region, ...
Authors:Nomura, Y, Sugiyama, S, Sakamoto, T, Miyakawa, S, Adachi, H, Takano, K, Murakami, S, Inoue, T, Mori, Y, Nakamura, Y, Matsumura, H.
Deposit date:2010-04-08
Release date:2010-11-10
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex
Nucleic Acids Res., 38, 2010
6PFQ
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BU of 6pfq by Molmil
Structure of Kluyveromyces marxianus Usb1
Descriptor: GLYCEROL, Uncharacterized protein YLR132C
Authors:Nomura, Y, Montemayor, E.J, Butcher, S.E.
Deposit date:2019-06-21
Release date:2019-12-11
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.
Nucleic Acids Res., 48, 2020
6PGL
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BU of 6pgl by Molmil
Structure of Kluyveromyces marxianus Usb1 with uridine monophosphate
Descriptor: 1,2-ETHANEDIOL, 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, GLYCEROL, ...
Authors:Nomura, Y, Montemayor, E.J, Butcher, S.E.
Deposit date:2019-06-24
Release date:2019-12-11
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.845 Å)
Cite:Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.
Nucleic Acids Res., 48, 2020
4U6M
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BU of 4u6m by Molmil
Crystal structure of DNA/RNA duplex obtained in the presence of Spermine
Descriptor: DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
Authors:Kondo, J, Nomura, Y, Kitahara, Y, Obika, S, Torigoe, H.
Deposit date:2014-07-29
Release date:2015-08-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.
Chem.Commun.(Camb.), 52, 2016
4U6K
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BU of 4u6k by Molmil
Crystal structure of DNA/RNA duplex containing 2'-4'-BNA-NC
Descriptor: COBALT HEXAMMINE(III), DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
Authors:Kondo, J, Nomura, Y, Kitahara, Y, Obika, S, Torigoe, H.
Deposit date:2014-07-29
Release date:2015-08-19
Last modified:2022-07-06
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.
Chem.Commun.(Camb.), 52, 2016
4U6L
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BU of 4u6l by Molmil
Crystal structure of DNA/RNA duplex obtained in the presence of [Co(NH3)6]Cl3 and SrCl2
Descriptor: COBALT HEXAMMINE(III), DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3'), ...
Authors:Kondo, J, Nomura, Y, Kitahara, Y, Obika, S, Torigoe, H.
Deposit date:2014-07-29
Release date:2015-08-19
Last modified:2022-07-06
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.
Chem.Commun.(Camb.), 52, 2016
3E54
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BU of 3e54 by Molmil
Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA
Descriptor: DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3'), ...
Authors:Nomura, N, Nomura, Y, Sussman, D, Stoddard, B.L.
Deposit date:2008-08-13
Release date:2008-12-30
Last modified:2021-11-10
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases
Nucleic Acids Res., 36, 2008
7MKT
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BU of 7mkt by Molmil
Crystal structure of r(GU)11G-NMM complex
Descriptor: N-METHYLMESOPORPHYRIN, POTASSIUM ION, RNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')
Authors:Bingman, C.A, Roschdi, S, Nomura, Y, Butcher, S.E.
Deposit date:2021-04-26
Release date:2022-11-02
Last modified:2023-02-08
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:An atypical RNA quadruplex marks RNAs as vectors for gene silencing.
Nat.Struct.Mol.Biol., 29, 2022
5YOY
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BU of 5yoy by Molmil
Crystal structure of the human tumor necrosis factor in complex with golimumab Fv
Descriptor: Golimumab heavy chain variable region, Golimumab light chain variable region, Tumor necrosis factor
Authors:Ono, M, Horita, S, Sato, Y, Nomura, Y, Iwata, S, Nomura, N.
Deposit date:2017-10-31
Release date:2018-05-09
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.727 Å)
Cite:Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab
Protein Sci., 27, 2018
6A94
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BU of 6a94 by Molmil
Crystal structure of 5-HT2AR in complex with zotepine
Descriptor: 2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-(3-chloranylbenzo[b][1]benzothiepin-5-yl)oxy-N,N-dimethyl-ethanamine, 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562, ...
Authors:Kimura, T.K, Asada, H, Inoue, A, Kadji, F.M.N, Im, D, Mori, C, Arakawa, T, Hirata, K, Nomura, Y, Nomura, N, Aoki, J, Iwata, S, Shimamura, T.
Deposit date:2018-07-11
Release date:2019-02-13
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine.
Nat.Struct.Mol.Biol., 26, 2019
6A93
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BU of 6a93 by Molmil
Crystal structure of 5-HT2AR in complex with risperidone
Descriptor: 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one, 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562, CHOLESTEROL, ...
Authors:Kimura, T.K, Asada, H, Inoue, A, Kadji, F.M.N, Im, D, Mori, C, Arakawa, T, Hirata, K, Nomura, Y, Nomura, N, Aoki, J, Iwata, S, Shimamura, T.
Deposit date:2018-07-11
Release date:2019-02-13
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine.
Nat.Struct.Mol.Biol., 26, 2019
4YBQ
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BU of 4ybq by Molmil
Rat GLUT5 with Fv in the outward-open form
Descriptor: Solute carrier family 2, facilitated glucose transporter member 5, antibody Fv fragment heavy chain, ...
Authors:Nomura, N, Shimamura, T, Iwata, S.
Deposit date:2015-02-19
Release date:2015-10-07
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.27 Å)
Cite:Structure and mechanism of the mammalian fructose transporter GLUT5
Nature, 526, 2015
4YB9
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BU of 4yb9 by Molmil
Crystal structure of the Bovine Fructose transporter GLUT5 in an open inward-facing conformation
Descriptor: Solute carrier family 2, facilitated glucose transporter member 5
Authors:Verdon, G, Kang, H.J, Iwata, S, Drew, D.
Deposit date:2015-02-18
Release date:2015-10-14
Last modified:2017-08-30
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structure and mechanism of the mammalian fructose transporter GLUT5.
Nature, 526, 2015
5B8C
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BU of 5b8c by Molmil
High resolution structure of the human PD-1 in complex with pembrolizumab Fv
Descriptor: Pembrolizumab heavy chain variable region (PemVH), Pembrolizumab light chain variable region (PemVL), Programmed cell death protein 1
Authors:Horita, S, Shimamura, T, Iwata, S, Nomura, N.
Deposit date:2016-06-14
Release date:2016-10-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.146 Å)
Cite:High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1
Sci Rep, 6, 2016
5AYG
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BU of 5ayg by Molmil
Crystal Structure of the Human ROR gamma Ligand Binding Domain With 3g
Descriptor: 3-[5-(2-cyclohexylethyl)-4-ethyl-1,2,4-triazol-3-yl]-N-naphthalen-1-yl-propanamide, Nuclear receptor ROR-gamma
Authors:Noguchi, M, Doi, S, Nomura, A, Kikuwaka, M, Murase, K, Hirata, K, Kamada, M, Adachi, T.
Deposit date:2015-08-20
Release date:2016-03-02
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:SAR Exploration Guided by LE and Fsp(3): Discovery of a Selective and Orally Efficacious ROR gamma Inhibitor
Acs Med.Chem.Lett., 7, 2016
6LBH
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BU of 6lbh by Molmil
Cryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions
Descriptor: Fab heavy chain, Fab light chain, Magnesium transporter MgtE
Authors:Hattori, M, Jin, F.
Deposit date:2019-11-14
Release date:2021-04-14
Last modified:2021-05-19
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:The structure of MgtE in the absence of magnesium provides new insights into channel gating.
Plos Biol., 19, 2021
8H78
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BU of 8h78 by Molmil
Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
Descriptor: (2~{R})-2-[[4-[(4-aminocarbonylphenyl)carbonylamino]phenyl]sulfonylamino]-5-[(2~{S},4~{S})-4-azanyl-2-[[(2~{S})-1-[[(2~{S})-1-[(5-azanyl-5-oxidanylidene-pentyl)amino]-5-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamoyl]pyrrolidin-1-yl]-5-oxidanylidene-pentanoic acid, CALCIUM ION, DIHYDROGENPHOSPHATE ION, ...
Authors:Kamitani, M, Takeuchi, T, Mima, M.
Deposit date:2022-10-19
Release date:2023-01-18
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold.
J.Med.Chem., 66, 2023
8HRX
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BU of 8hrx by Molmil
Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex
Descriptor: Fab heavy chain from antibody IgG clone number YN9048, Fab light chain from antibody IgG clone number YN9048, PreS1 protein (Fragment), ...
Authors:Asami, J, Shimizu, T, Ohto, U.
Deposit date:2022-12-16
Release date:2024-01-17
Last modified:2024-01-31
Method:ELECTRON MICROSCOPY (2.89 Å)
Cite:Structural basis of hepatitis B virus receptor binding.
Nat.Struct.Mol.Biol., 2024
8HRY
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BU of 8hry by Molmil
Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex
Descriptor: Fab heavy chain from antibody IgG clone number YN9016, Fab light chain from antibody IgG clone number YN9016, Large S protein (Fragment), ...
Authors:Asami, J, Shimizu, T, Ohto, U.
Deposit date:2022-12-16
Release date:2024-01-17
Last modified:2024-01-31
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Structural basis of hepatitis B virus receptor binding.
Nat.Struct.Mol.Biol., 2024
7VAF
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BU of 7vaf by Molmil
Cryo-EM structure of Rat NTCP complexed with YN69202Fab
Descriptor: Fab heavy chain from antibody IgG clone number YN69202, Fab light chain from antibody IgG clone number YN69202, Sodium/bile acid cotransporter
Authors:Asami, J, Shimizu, T, Ohto, U.
Deposit date:2021-08-29
Release date:2022-05-25
Last modified:2022-07-13
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Structure of the bile acid transporter and HBV receptor NTCP.
Nature, 606, 2022

 

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