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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Fujinaga, M."

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Search Summary

This query matches 25 Structures.

Refinements

Structure Determination Methodology

experimental (25)

Scientific Name of Source Organism

	Homo sapiens (20)
	Severe acute respiratory syndrome coronavirus 2 (10)
	Escherichia coli (6)
	Sendai virus (Z) (1)

Taxonomy

	Eukaryota (20)
	Riboviria (11)
	Bacteria (6)

Experimental Method

	ELECTRON MICROSCOPY (20)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

	Protein (25)
	RNA (10)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (8)
	2.5 - 3.0 (11)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	2015 - 2019 (3)
	2020 - 2024 (22)

Enzyme Classification Name

	Hydrolases (6)
	Lyases (4)
	Transferases (3)

Symmetry Type

	Asymmetric (19)
	Cyclic (5)

SCOP Classification

	Alpha and beta proteins (a+b) (1)
	All alpha proteins (2)

AllSelected

1 to 25 of 25 Structures

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3WWT	Download File View File

Crystal Structure of the Y3:STAT1ND complex

Oda, K., Sakaguchi, T., Matoba, Y.

(2015) J Virol 89: 11487-11499

Released	2015-07-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Sendai virus (Z)
Macromolecule	C' protein (protein) Signal transducer and activator of transcription 1-alpha/beta (protein)
Unique Ligands	CA

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4Y2B	Download File View File

Co-crystal structure of 3-ethyl-2-(isopropylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one bound to PDE7A

Endo, Y., Kawai, K., Asano, T., Amano, S., Asanuma, Y., Sawada, K., Onodera, Y., Ueo, N., Takahashi, N., Sonoda, Y., Kamei, N., Irie, T.

(2015) Bioorg Med Chem Lett 25: 1910-1914

Released	2015-04-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A (protein)
Unique Ligands	EPK, MG, ZN

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5ZZ4	Download File View File

Crystal structure of bruton's tyrosine kinase in complex with inhibitor 2e

Kawahata, W., Asami, T., Irie, T., Kiyoi, T., Taniguchi, H., Asamitsu, Y., Inoue, T., Miyake, T., Sawa, M.

(2018) J Med Chem 61: 8917-8933

Released	2018-09-26
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase BTK (protein)
Unique Ligands	9M3

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6KC5	Download File View File

HOIP-HOIPIN1 complex

Sato, Y., Fukai, S.

(2020) Commun Biol 3: 163-163

Released	2020-04-15
Method	X-RAY DIFFRACTION 1.543 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF31 (protein)
Unique Ligands	D5U, EPE, GOL, ZN

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6KC6	Download File View File

HOIP-HOIPIN8 complex

Sato, Y., Fukai, S.

(2020) Commun Biol 3: 163-163

Released	2020-04-15
Method	X-RAY DIFFRACTION 2.123 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF31 (protein)
Unique Ligands	CL, D60, GOL, ZN

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7Y7C	Download File View File

Structure of the Bacterial Ribosome with human tRNA Asp(G34) and mRNA(GAU)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-10-25
Method	ELECTRON MICROSCOPY 2.51 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	MG

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7Y7D	Download File View File

Structure of the Bacterial Ribosome with human tRNA Asp(Q34) and mRNA(GAU)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-10-25
Method	ELECTRON MICROSCOPY 2.58 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	MG

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7Y7E	Download File View File

Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-10-25
Method	ELECTRON MICROSCOPY 2.41 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	MAN, MG

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7Y7F	Download File View File

Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAC)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-10-25
Method	ELECTRON MICROSCOPY 2.43 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	MAN, MG

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7Y7G	Download File View File

Structure of the Bacterial Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-10-25
Method	ELECTRON MICROSCOPY 2.34 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	GAL, MG

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7Y7H	Download File View File

Structure of the Bacterial Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAC)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-10-25
Method	ELECTRON MICROSCOPY 2.51 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	GAL, MG

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8GS6	Download File View File

Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1)

Anraku, Y., Tabata-Sasaki, K., Kita, S., Fukuhara, H., Maenaka, K., Hashiguchi, T.

(2022) Cell Host Microbe 30: 1540-1555.e15

Released	2022-10-26
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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8JDJ	Download File View File

Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-12-06
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 73 Unique nucleic acid chains: 6
Unique Ligands	MG, ZN

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8JDK	Download File View File

Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-12-06
Method	ELECTRON MICROSCOPY 2.26 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 73 Unique nucleic acid chains: 6
Unique Ligands	MAN, MG, ZN

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8JDL	Download File View File

Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-12-06
Method	ELECTRON MICROSCOPY 2.42 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 73 Unique nucleic acid chains: 6
Unique Ligands	GAL, MG, ZN

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8JDM	Download File View File

Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (rotated state)

Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.

(2023) Cell 186: 5517

Released	2023-12-06
Method	ELECTRON MICROSCOPY 2.67 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 73 Unique nucleic acid chains: 6
Unique Ligands	GAL, MG, ZN

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8JYK	Download File View File

Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 1)

Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.

(2024) Nat Commun 15: 1176-1176

Released	2024-01-03
Method	ELECTRON MICROSCOPY 2.59 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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8JYM	Download File View File

Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2)

Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.

(2024) Nat Commun 15: 1176-1176

Released	2024-01-03
Method	ELECTRON MICROSCOPY 2.79 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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8JYN	Download File View File

Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)

Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.

(2024) Nat Commun 15: 1176-1176

Released	2024-01-03
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8JYO	Download File View File

Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state)

Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.

(2024) Nat Commun 15: 1176-1176

Released	2024-01-03
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8JYP	Download File View File

Structure of SARS-CoV-2 XBB.1.5 spike RBD in complex with ACE2

Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.

(2024) Nat Commun 15: 1176-1176

Released	2024-01-03
Method	ELECTRON MICROSCOPY 3.38 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8WMD	Download File View File

Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-2 state)

Nomai, T., Anraku, Y., Kita, S., Hashiguchi, T., Maenaka, K.

(2024) Microbiol Immunol 68: 305-330

Released	2024-04-24
Method	ELECTRON MICROSCOPY 2.71 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG

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8WMF	Download File View File

Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-1 state)

Nomai, T., Anraku, Y., Kita, S., Hashiguchi, T., Maenaka, K.

(2024) Microbiol Immunol 68: 305-330

Released	2024-04-24
Method	ELECTRON MICROSCOPY 2.51 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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8XLM	Download File View File

Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state)

Nomai, T., Anraku, Y., Kita, S., Hashiguchi, T., Maenaka, K.

(2024) Microbiol Immunol 68: 305-330

Released	2024-05-01
Method	ELECTRON MICROSCOPY 3.22 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8XLN	Download File View File

Structure of the SARS-CoV-2 EG.5.1 spike RBD in complex with ACE2

Nomai, T., Anraku, Y., Kita, S., Hashiguchi, T., Maenaka, K.

(2024) Microbiol Immunol 68: 305-330

Released	2024-05-01
Method	ELECTRON MICROSCOPY 3.78 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

1 to 25 of 25 Structures

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