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8WDV
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BU of 8wdv by Molmil
Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by Ca2+-DEAE
Descriptor: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate, Antenna complex alpha/beta subunit, ...
Authors:Tani, K, Kanno, R, Harada, A, Kobayashi, A, Minamino, A, Nakamura, N, Ji, X.-C, Purba, E.R, Hall, M, Yu, L.-J, Madigan, M.T, Mizoguchi, A, Iwasaki, K, Humbel, B.M, Kimura, Y, Wang-Otomo, Z.-Y.
Deposit date:2023-09-16
Release date:2024-02-21
Method:ELECTRON MICROSCOPY (2.24 Å)
Cite:High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum
Commun Biol, 7, 2024
8WDU
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BU of 8wdu by Molmil
Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density
Descriptor: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate, Antenna complex alpha/beta subunit, ...
Authors:Tani, K, Kanno, R, Harada, A, Kobayashi, A, Minamino, A, Nakamura, N, Ji, X.-C, Purba, E.R, Hall, M, Yu, L.-J, Madigan, M.T, Mizoguchi, A, Iwasaki, K, Humbel, B.M, Kimura, Y, Wang-Otomo, Z.-Y.
Deposit date:2023-09-16
Release date:2024-02-21
Method:ELECTRON MICROSCOPY (2.24 Å)
Cite:High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum
Commun Biol, 7, 2024
5GJE
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BU of 5gje by Molmil
Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1
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:Matoba, K, Mihara, E, Tamura-Kawakami, K, Hirai, H, Thompson, S, Iwasaki, K, Takagi, J.
Deposit date:2016-06-29
Release date:2017-01-18
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (21 Å)
Cite:Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1
Cell Rep, 18, 2017
6S2C
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BU of 6s2c by Molmil
Acquired functional capsid structures in metazoan totivirus-like dsRNA virus.
Descriptor: Capsid protein
Authors:Okamoto, K, Larsson, S.D.D, Maia, R.N.C.F, Murata, K, Hajdu, J, Iwasaki, K, Miyazaki, N.
Deposit date:2019-06-20
Release date:2020-04-29
Last modified:2020-08-19
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus.
Structure, 28, 2020
6RVV
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BU of 6rvv by Molmil
Structure of left-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.
Descriptor: GOLD ION, Transcription attenuation protein MtrB
Authors:Malay, A.D, Miyazaki, N, Biela, A.P, Iwasaki, K, Heddle, J.G.
Deposit date:2019-06-03
Release date:2019-06-12
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:An ultra-stable gold-coordinated protein cage displaying reversible assembly.
Nature, 569, 2019
6RVW
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BU of 6rvw by Molmil
Structure of right-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.
Descriptor: GOLD ION, Transcription attenuation protein MtrB
Authors:Malay, A.D, Miyazaki, N, Biela, A.P, Iwasaki, K, Heddle, J.G.
Deposit date:2019-06-03
Release date:2019-06-12
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:An ultra-stable gold-coordinated protein cage displaying reversible assembly.
Nature, 569, 2019
6KNC
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BU of 6knc by Molmil
PolD-PCNA-DNA (form B)
Descriptor: DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ...
Authors:Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y.
Deposit date:2019-08-05
Release date:2020-08-05
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (9.3 Å)
Cite:Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
6KNB
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BU of 6knb by Molmil
PolD-PCNA-DNA (form A)
Descriptor: DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ...
Authors:Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y.
Deposit date:2019-08-05
Release date:2020-08-05
Last modified:2021-02-17
Method:ELECTRON MICROSCOPY (6.9 Å)
Cite:Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
6IUK
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BU of 6iuk by Molmil
Cryo-EM structure of Murine Norovirus capsid
Descriptor: Major capsid protein VP1
Authors:Song, C, Miyazaki, N, Iwasaki, K, Katayama, K, Murata, K.
Deposit date:2018-11-28
Release date:2020-02-26
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Dynamic rotation of the protruding domain enhances the infectivity of norovirus.
Plos Pathog., 16, 2020
6KLW
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BU of 6klw by Molmil
Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with long stem
Descriptor: CALCIUM ION, Iota toxin component Ia, Iota toxin component Ib
Authors:Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H.
Deposit date:2019-07-30
Release date:2020-01-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
Nat.Struct.Mol.Biol., 27, 2020
6KLX
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BU of 6klx by Molmil
Pore structure of Iota toxin binding component (Ib)
Descriptor: CALCIUM ION, Iota toxin component Ib
Authors:Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H.
Deposit date:2019-07-30
Release date:2020-01-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
Nat.Struct.Mol.Biol., 27, 2020
6KLO
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BU of 6klo by Molmil
Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with short stem
Descriptor: CALCIUM ION, Iota toxin component Ia, Iota toxin component Ib
Authors:Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H.
Deposit date:2019-07-30
Release date:2020-01-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
Nat.Struct.Mol.Biol., 27, 2020
6LXV
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BU of 6lxv by Molmil
Cryo-EM structure of phosphoketolase from Bifidobacterium longum
Descriptor: CALCIUM ION, Phosphoketolase, THIAMINE DIPHOSPHATE
Authors:Nakata, K, Miyazaki, N, Yamaguchi, H, Hirose, M, Miyano, H, Mizukoshi, T, Kashiwagi, T, Iwasaki, K.
Deposit date:2020-02-12
Release date:2021-02-17
Last modified:2022-10-12
Method:ELECTRON MICROSCOPY (2.1 Å)
Cite:High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis.
J.Struct.Biol., 214, 2022
7DOD
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BU of 7dod by Molmil
Capsid structure of human sapovirus
Descriptor: Calicivirin
Authors:Miyazaki, N, Murakami, K, Oka, T, Iwasaki, K, Katayama, K, Murata, K.
Deposit date:2020-12-14
Release date:2021-12-15
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy
To Be Published
1IQ4
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BU of 1iq4 by Molmil
5S-RRNA BINDING RIBOSOMAL PROTEIN L5 FROM BACILLUS STEAROTHERMOPHILUS
Descriptor: 50S RIBOSOMAL PROTEIN L5
Authors:Nakashima, T, Yao, M, Kawamura, S, Iwasaki, K, Kimura, M, Tanaka, I.
Deposit date:2001-06-13
Release date:2001-06-27
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.
RNA, 7, 2001
7DOU
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BU of 7dou by Molmil
Trimeric cement protein structure of Helicobacter pylori bacteriophage KHP40
Descriptor: Cement protein gp16
Authors:Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N.
Deposit date:2020-12-17
Release date:2021-10-27
Last modified:2022-02-23
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.
Structure, 30, 2022
7DN2
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BU of 7dn2 by Molmil
Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30
Descriptor: Cement protein gp15, Major structural protein ORF14
Authors:Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N.
Deposit date:2020-12-08
Release date:2021-10-27
Last modified:2022-02-23
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.
Structure, 30, 2022
7F2P
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BU of 7f2p by Molmil
The head structure of Helicobacter pylori bacteriophage KHP40
Descriptor: Cement protein gp16, KHP40 MCP
Authors:Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N.
Deposit date:2021-06-13
Release date:2021-10-27
Last modified:2022-02-23
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.
Structure, 30, 2022
7WU9
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BU of 7wu9 by Molmil
Cryo-EM structure of the human EP3-Gi signaling complex
Descriptor: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(i) subunit alpha-1, ...
Authors:Suno, R, Sugita, Y, Morimoto, K, Iwasaki, K, Kato, T, Kobayashi, T.
Deposit date:2022-02-07
Release date:2022-08-17
Last modified:2023-10-04
Method:ELECTRON MICROSCOPY (3.375 Å)
Cite:Structural insights into the G protein selectivity revealed by the human EP3-G i signaling complex.
Cell Rep, 40, 2022
7WMP
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BU of 7wmp by Molmil
Tail structure of Helicobacter pylori bacteriophage KHP30
Descriptor: Adaptor protein gp12, Nozzle protein gp25, Portal protein
Authors:Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N.
Deposit date:2022-01-15
Release date:2023-03-01
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Cryo-EM structure of Helicobacter pylori bacteriophage KHP30
To Be Published
7X30
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BU of 7x30 by Molmil
Capsid structure of Staphylococcus jumbo bacteriophage S6
Descriptor: Hoc-like protein ORF90, Major structural protein ORF12
Authors:Koibuchi, W, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N.
Deposit date:2022-02-27
Release date:2023-12-06
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Capsid structure of Staphylococcus jumbo bacteriophage S6
To Be Published
3VKF
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BU of 3vkf by Molmil
Crystal Structure of Neurexin 1beta/Neuroligin 1 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Neurexin-1-beta, ...
Authors:Tanaka, H, Miyazaki, N, Nogi, T, Iwasaki, K, Takagi, J.
Deposit date:2011-11-15
Release date:2012-08-01
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Higher-order architecture of cell adhesion mediated by polymorphic synaptic adhesion molecules neurexin and neuroligin.
Cell Rep, 2, 2012
6AB5
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BU of 6ab5 by Molmil
Cryo-EM structure of T=1 Penaeus vannamei nodavirus
Descriptor: Capsid protein
Authors:Chen, N.C, Miyazaki, N, Yoshimura, M, Guan, H.H, Lin, C.C, Iwasaki, K, Chen, C.J.
Deposit date:2018-07-20
Release date:2019-03-20
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Commun Biol, 2, 2019
6AB6
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BU of 6ab6 by Molmil
Cryo-EM structure of T=3 Penaeus vannamei nodavirus
Descriptor: CALCIUM ION, Capsid protein
Authors:Chen, N.C, Miyazaki, N, Yoshimura, M, Guan, H.H, Lin, C.C, Iwasaki, K, Chen, C.J.
Deposit date:2018-07-20
Release date:2019-03-20
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Commun Biol, 2, 2019
4V60
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BU of 4v60 by Molmil
The structure of rat liver vault at 3.5 angstrom resolution
Descriptor: Major vault protein
Authors:Kato, K, Zhou, Y, Tanaka, H, Yao, M, Yamashita, E, Yoshimura, M, Tsukihara, T.
Deposit date:2008-10-24
Release date:2014-07-09
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:The structure of rat liver vault at 3.5 angstrom resolution
Science, 323, 2009

 

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