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3GNE
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BU of 3gne by Molmil
Crystal structure of alginate lyase vAL-1 from Chlorella virus
Descriptor: CITRATE ANION, GLYCEROL, VAL-1
Authors:Ogura, K, Yamasaki, M, Hashidume, T, Yamada, T, Mikami, B, Hashimoto, W, Murata, K.
Deposit date:2009-03-17
Release date:2009-10-20
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action
J.Biol.Chem., 284, 2009
7C86
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BU of 7c86 by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2020-05-28
Release date:2021-04-07
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
5H6U
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BU of 5h6u by Molmil
Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide
Descriptor: AlgQ2, CALCIUM ION, beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid
Authors:Uenishi, K, Kaneko, A, Maruyama, Y, Mikami, B, Murata, K, Hashimoto, W.
Deposit date:2016-11-15
Release date:2017-08-09
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.006 Å)
Cite:A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate
J. Biol. Chem., 292, 2017
5H71
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BU of 5h71 by Molmil
Structure of alginate-binding protein AlgQ2 in complex with an alginate trisaccharide
Descriptor: 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, AlgQ2, CALCIUM ION, ...
Authors:Uenishi, K, Kaneko, A, Maruyama, Y, Mikami, B, Murata, K, Hashimoto, W.
Deposit date:2016-11-15
Release date:2017-08-09
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.549 Å)
Cite:A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate
J. Biol. Chem., 292, 2017
8XBI
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BU of 8xbi by Molmil
Human GPR34 -Gi complex bound to M1, receptor focused
Descriptor: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Probable G-protein coupled receptor 34
Authors:Kawahara, R, Shihoya, W, Nureki, O.
Deposit date:2023-12-06
Release date:2023-12-27
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.06 Å)
Cite:Structural basis for lysophosphatidylserine recognition by GPR34.
Nat Commun, 15, 2024
8XBH
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BU of 8xbh by Molmil
Human GPR34 -Gi complex bound to M1
Descriptor: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, 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, ...
Authors:Kawahara, R, Shihoya, W, Nureki, O.
Deposit date:2023-12-06
Release date:2023-12-27
Last modified:2024-10-30
Method:ELECTRON MICROSCOPY (2.83 Å)
Cite:Structural basis for lysophosphatidylserine recognition by GPR34.
Nat Commun, 15, 2024
1KWH
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BU of 1kwh by Molmil
Structure Analysis AlgQ2, a Macromolecule(alginate)-Binding Periplasmic Protein of Sphingomonas sp. A1.
Descriptor: CALCIUM ION, Macromolecule-Binding Periplasmic Protein
Authors:Momma, K, Mikami, B, Mishima, Y, Hashimoto, W, Murata, K.
Deposit date:2002-01-29
Release date:2002-02-13
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution.
J.Mol.Biol., 316, 2002
8XBG
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BU of 8xbg by Molmil
Human GPR34 -Gi complex bound to S3E-LysoPS, receptor focused
Descriptor: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Probable G-protein coupled receptor 34
Authors:Kawahara, R, Shihoya, W, Nureki, O.
Deposit date:2023-12-06
Release date:2024-05-15
Method:ELECTRON MICROSCOPY (3.43 Å)
Cite:Structural basis for lysophosphatidylserine recognition by GPR34.
Nat Commun, 15, 2024
8XBE
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BU of 8xbe by Molmil
Human GPR34 -Gi complex bound to S3E-LysoPS
Descriptor: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, 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, ...
Authors:Kawahara, R, Shihoya, W, Nureki, O.
Deposit date:2023-12-06
Release date:2024-05-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for lysophosphatidylserine recognition by GPR34.
Nat Commun, 15, 2024
7DB6
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BU of 7db6 by Molmil
human melatonin receptor MT1 - Gi1 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:Okamoto, H.H, Kusakizako, T, Shihioya, W, Yamashita, K, Nishizawa, T, Nureki, O.
Deposit date:2020-10-19
Release date:2021-08-18
Last modified:2022-02-16
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cryo-EM structure of the human MT 1 -G i signaling complex.
Nat.Struct.Mol.Biol., 28, 2021
1HV6
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BU of 1hv6 by Molmil
CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III COMPLEXED WITH TRISACCHARIDE PRODUCT.
Descriptor: 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-D-glucopyranuronic acid, ALGINATE LYASE, SULFATE ION
Authors:Yoon, H.-J, Hashimoto, W, Miyake, O, Murata, K, Mikami, B.
Deposit date:2001-01-08
Release date:2001-05-02
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.
J.Mol.Biol., 307, 2001
7D3S
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BU of 7d3s by Molmil
Human SECR in complex with an engineered Gs heterotrimer
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(s) subunit alpha isoforms short, ...
Authors:Fukuhara, S, Kobayashi, K, Kusakizako, T, Shihoya, W, Nureki, O.
Deposit date:2020-09-20
Release date:2020-11-04
Last modified:2020-12-30
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structure of the human secretin receptor coupled to an engineered heterotrimeric G protein.
Biochem.Biophys.Res.Commun., 533, 2020
7CJ3
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BU of 7cj3 by Molmil
Crystal structure of the transmembrane domain of Salpingoeca rosetta rhodopsin phosphodiesterase
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Phosphodiesterase, RETINAL
Authors:Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O.
Deposit date:2020-07-09
Release date:2020-11-25
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
2RGK
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BU of 2rgk by Molmil
Functional annotation of Escherichia coli yihS-encoded protein
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Uncharacterized sugar isomerase yihS
Authors:Itoh, T, Mikami, B, Hashimoto, W, Murata, K.
Deposit date:2007-10-03
Release date:2008-08-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase
J.Mol.Biol., 377, 2008
7D7Q
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BU of 7d7q by Molmil
Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Phosphodiesterase, RETINAL
Authors:Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O.
Deposit date:2020-10-05
Release date:2020-11-18
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
7D7P
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BU of 7d7p by Molmil
Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, ...
Authors:Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O.
Deposit date:2020-10-05
Release date:2020-11-18
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
3K8W
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BU of 3k8w by Molmil
Crysatl structure of a bacterial cell-surface flagellin N20C45
Descriptor: Flagellin homolog
Authors:Maruyama, Y, Momma, M, Hashimoto, W, Murata, K.
Deposit date:2009-10-15
Release date:2010-10-06
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of N- and C-terminal regions of flagellin
To be Published
3K3T
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BU of 3k3t by Molmil
E185A mutant of peptidoglycan hydrolase from Sphingomonas sp. A1
Descriptor: Peptidoglycan hydrolase FlgJ, SULFATE ION
Authors:Maruyama, Y, Ochiai, A, Itoh, T, Mikami, B, Hashimoto, W, Murata, K.
Deposit date:2009-10-04
Release date:2010-07-14
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1
J.Basic Microbiol., 50, 2010
2GH4
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BU of 2gh4 by Molmil
YteR/D143N/dGalA-Rha
Descriptor: 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose, Putative glycosyl hydrolase yteR
Authors:Itoh, T, Ochiai, A, Mikami, B, Hashimoto, W, Murata, K.
Deposit date:2006-03-25
Release date:2006-08-29
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate
Biochem.Biophys.Res.Commun., 347, 2006
2FUZ
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BU of 2fuz by Molmil
UGL hexagonal crystal structure without glycine and DTT molecules
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Unsaturated glucuronyl hydrolase
Authors:Itoh, T, Hashimoto, W, Mikami, B, Murata, K.
Deposit date:2006-01-28
Release date:2006-05-30
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1
Biochem.Biophys.Res.Commun., 344, 2006
2FV0
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BU of 2fv0 by Molmil
UGL_D88N/dGlcA-Glc-Rha-Glc
Descriptor: 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-4)-beta-D-glucopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-beta-D-glucopyranose, Unsaturated glucuronyl hydrolase
Authors:Itoh, T, Hashimoto, W, Mikami, B, Murata, K.
Deposit date:2006-01-28
Release date:2006-05-30
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1
Biochem.Biophys.Res.Commun., 344, 2006
2FV1
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BU of 2fv1 by Molmil
UGL_D88N/dGlcA-GlcNAc
Descriptor: 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose, Unsaturated glucuronyl hydrolase
Authors:Itoh, T, Hashimoto, W, Mikami, B, Murata, K.
Deposit date:2006-01-28
Release date:2006-05-30
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1
Biochem.Biophys.Res.Commun., 344, 2006
5GX7
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BU of 5gx7 by Molmil
Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-6 position of GalNAc
Descriptor: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose, CALCIUM ION, Extracellular solute-binding protein family 1
Authors:Oiki, S, Mikami, B, Murata, K, Hashimoto, W.
Deposit date:2016-09-15
Release date:2017-07-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.991 Å)
Cite:A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Sci Rep, 7, 2017
5GUB
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BU of 5gub by Molmil
Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide
Descriptor: 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose, ...
Authors:Oiki, S, Mikami, B, Murata, K, Hashimoto, W.
Deposit date:2016-08-26
Release date:2017-07-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Sci Rep, 7, 2017
4F13
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BU of 4f13 by Molmil
Alginate lyase A1-III Y246F complexed with tetrasaccharide
Descriptor: 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, Alginate lyase, beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid
Authors:Mikami, B, Ban, M, Suzuki, S, Yoon, H.-J, Miyake, O, Yamasaki, M, Ogura, K, Maruyama, Y, Hashimoto, W, Murata, K.
Deposit date:2012-05-06
Release date:2012-06-27
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.208 Å)
Cite:Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III
Acta Crystallogr.,Sect.D, 68, 2012

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