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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Iida, T."

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

	Enterococcus hirae ATCC 9790 (4)
	Escherichia coli (4)
	Vibrio cholerae (3)
	Clostridium perfringens (2)
	Homo sapiens (2)
	synthetic construct (2)

Taxonomy

	Bacteria (13)
	Eukaryota (2)
	other sequences (2)

Experimental Method

X-RAY DIFFRACTION (15)

Polymer Entity Type

Protein (15)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (1)
	1.5 - 2.0 (5)
	2.0 - 2.5 (2)
	2.5 - 3.0 (1)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)
	4.0 - 4.5 (2)

Release Date

	2010 - 2014 (1)
	2015 - 2019 (5)
	2020 - 2024 (9)

Enzyme Classification Name

	Translocases (4)
	Hydrolases (2)

Symmetry Type

	Asymmetric (9)
	Cyclic (6)

SCOP Classification

Alpha and beta proteins (a+b) (2)

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1 to 15 of 15 Structures

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3VOR	Download File View File

Crystal Structure Analysis of the CofA

Fukakusa, S., Kawahara, K., Nakamura, S., Iwasita, T., Baba, S., Nishimura, M., Kobayashi, Y., Honda, T., Iida, T., Taniguchi, T., Ohkubo, T.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1418-1429

Released	2012-09-26
Method	X-RAY DIFFRACTION 0.9 Å
Organisms	Escherichia coli
Macromolecule	CFA/III pilin (protein)

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5AX6	Download File View File

The crystal structure of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli.

Kawahara, K., Oki, K., Fukaksua, F., Maruno, T., Kobayashi, Y., Daisuke, M., Taniguchi, T., Honda, T., Iida, T., Nakamura, S., Ohkubo, T.

(2016) J Mol Biology 428: 1209-1226

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Escherichia coli
Macromolecule	CofB (protein)
Unique Ligands	ACT

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5H03	Download File View File

Crystal structure of an ADP-ribosylating toxin BECa from C. perfringens

Kawahara, K., Yonogi, S., Munetomo, R., Oki, H., Yoshida, T., Ohkubo, T., Kumeda, Y., Matsuda, S., Kodama, T., Iida, T., Nakamura, S.

(2016) Biochem Biophys Res Commun 480: 261-267

Released	2016-11-02
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Clostridium perfringens
Macromolecule	Binary enterotoxin of Clostridium perfringens component a (protein)

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5H04	Download File View File

Crystal structure of an ADP-ribosylating toxin BECa of a novel binary enterotoxin of C. perfringens with NADH

Kawahara, K., Yonogi, S., Munetomo, R., Oki, H., Yoshida, T., Ohkubo, T., Kumeda, Y., Matsuda, S., Kodama, T., Iida, T., Nakamura, S.

(2016) Biochem Biophys Res Commun 480: 261-267

Released	2016-11-02
Method	X-RAY DIFFRACTION 1.825 Å
Organisms	Clostridium perfringens
Macromolecule	Binary enterotoxin of Clostridium perfringens component a (protein)
Unique Ligands	NAI

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5YPZ	Download File View File

Crystal structure of minor pilin CofB from CFA/III complexed with N-terminal peptide fragment of CofJ

Oki, H., Kawahara, K., Maruno, T., Imai, T., Muroga, Y., Fukakusa, S., Iwashita, T., Kobayashi, Y., Matsuda, S., Kodama, T., Iida, T., Yoshida, T., Ohkubo, T., Nakamura, S.

(2018) Proc Natl Acad Sci U S A 115: 7422-7427

Released	2018-06-27
Method	X-RAY DIFFRACTION 3.521 Å
Organisms	Escherichia coli
Macromolecule	CofB (protein) CofJ (protein)

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5YQ0	Download File View File

Crystal structure of secreted protein CofJ from ETEC.

Oki, H., Kawahara, K., Maruno, T., Imai, T., Muroga, Y., Fukakusa, S., Iwashita, T., Kobayashi, Y., Matsuda, S., Kodama, T., Iida, T., Yoshida, T., Ohkubo, T., Nakamura, S.

(2018) Proc Natl Acad Sci U S A 115: 7422-7427

Released	2018-06-27
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Escherichia coli
Macromolecule	CofJ (protein)
Unique Ligands	CA

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7COQ	Download File View File

Hexameric Ring Complex of Engineered V1-ATPase bound to AMP-PNP: A3(De)3_(ANP)1cat

Kosugi, T., Tanabe, M., Koga, N.

To be published

Released	2021-08-11
Method	X-RAY DIFFRACTION 3.44 Å
Organisms	Enterococcus hirae ATCC 9790
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein)
Unique Ligands	ANP, MG

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7W63	Download File View File

Crystal structure of minor pilin TcpB from Vibrio cholerae

Oki, H., Kawahara, K., Iimori, M., Imoto, Y., Maruno, T., Uchiyama, S., Muroga, Y., Yoshida, A., Yoshida, T., Ohkubo, T., Matsuda, S., Iida, T., Nakamura, S.

(2022) Sci Adv 8: eabo3013-eabo3013

Released	2022-11-09
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Vibrio cholerae
Macromolecule	Toxin-coregulated pilus biosynthesis protein B (protein)
Unique Ligands	SO4

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7W64	Download File View File

Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with N-terminal peptide fragment of TcpF

Oki, H., Kawahara, K., Iimori, M., Imoto, Y., Maruno, T., Uchiyama, S., Muroga, Y., Yoshida, A., Yoshida, T., Ohkubo, T., Matsuda, S., Iida, T., Nakamura, S.

(2022) Sci Adv 8: eabo3013-eabo3013

Released	2022-11-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Vibrio cholerae
Macromolecule	TcpF (protein) Toxin-coregulated pilus biosynthesis protein B (protein)
Unique Ligands	1PE, CA, CL

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7W65	Download File View File

Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with secreted protein TcpF

Oki, H., Kawahara, K., Iimori, M., Imoto, Y., Maruno, T., Uchiyama, S., Muroga, Y., Yoshida, A., Yoshida, T., Ohkubo, T., Matsuda, S., Iida, T., Nakamura, S.

(2022) Sci Adv 8: eabo3013-eabo3013

Released	2022-11-09
Method	X-RAY DIFFRACTION 4.05 Å
Organisms	Vibrio cholerae
Macromolecule	Toxin coregulated pilus biosynthesis protein F (protein) Toxin-coregulated pilus biosynthesis protein B (protein)

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7YUZ	Download File View File

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784

Irie, M., Fukami, T.A., Tanada, M., Ohta, A., Torizawa, T.

(2023) J Am Chem Soc 145: 24035-24051

Released	2023-07-26
Method	X-RAY DIFFRACTION 1.878 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	AP8784 (protein) Isoform 2B of GTPase KRas (protein)
Unique Ligands	GDP, IOD, MG

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7YV1	Download File View File

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab

Irie, M., Fukami, T.A., Matsuo, A., Saka, K., Nishimura, M., Saito, H., Torizawa, T., Tanada, M., Ohta, A.

(2023) J Am Chem Soc 145: 24035-24051

Released	2023-07-26
Method	X-RAY DIFFRACTION 1.454 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Isoform 2B of GTPase KRas (protein) KA30L Fab H-chain (protein) KA30L Fab L-chain (protein) LUNA18 (protein)
Unique Ligands	GDP, MG

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8IGU	Download File View File

Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty

Kosugi, T., Tanabe, M., Koga, N.

(2023) Nat Chem 15: 1591-1598

Released	2023-07-12
Method	X-RAY DIFFRACTION 2.77 Å
Organisms	Enterococcus hirae ATCC 9790
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein)

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8IGV	Download File View File

Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP-Pi)1cat(ADP)2cat,2non-cat

Kosugi, T., Tanabe, M., Koga, N.

(2023) Nat Chem 15: 1591-1598

Released	2023-07-12
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Enterococcus hirae ATCC 9790
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein)
Unique Ligands	ADP, MG, PO4

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8IGW	Download File View File

Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat

Kosugi, T., Tanabe, M., Koga, N.

(2023) Nat Chem 15: 1591-1598

Released	2023-07-12
Method	X-RAY DIFFRACTION 4.2 Å
Organisms	Enterococcus hirae ATCC 9790
Macromolecule	V-type sodium ATPase catalytic subunit A (protein) V-type sodium ATPase subunit B (protein)
Unique Ligands	ADP, MG