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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Akagi, M."

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Search Summary

This query matches 23 Structures.

Refinements

Structure Determination Methodology

experimental (23)

Scientific Name of Source Organism

	Homo sapiens (19)
	Mus musculus (9)
	Saccharomyces cerevisiae (3)
	Bos taurus (1)
	Dendroaspis angusticeps (1)
	Human betaherpesvirus 5 (1)
	Tequatrovirus T4 (1)

Taxonomy

	Eukaryota (23)
	Duplodnaviria (2)

Experimental Method

	ELECTRON MICROSCOPY (13)
	X-RAY DIFFRACTION (10)

Polymer Entity Type

Protein (23)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (2)
	2.5 - 3.0 (5)
	3.0 - 3.5 (8)
	3.5 - 4.0 (4)
	4.0 - 4.5 (3)

Release Date

	2005 - 2009 (1)
	2015 - 2019 (12)
	2020 - 2024 (10)

Enzyme Classification Name

	Hydrolases (8)
	Transferases (3)

Membrane Protein Annotation

	PDBTM (20)
	MemProtMD (16)
	OPM (13)
	mpstruc (11)

Symmetry Type

	Asymmetric (16)
	Cyclic (6)
	Dihedral (1)

SCOP Classification

	All beta proteins (2)
	All alpha proteins (1)
	Artifacts (1)
	Small proteins (1)

AllSelected

1 to 23 of 23 Structures

Page 1 of 1

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2ZW3 \| pdb_00002zw3	Download File View File

Structure of the connexin-26 gap junction channel at 3.5 angstrom resolution

Maeda, S., Nakagawa, S., Suga, M., Yamashita, E., Oshima, A., Fujiyoshi, Y., Tsukihara, T.

(2009) Nature 458: 597-602

Released	2009-04-07
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Homo sapiens
Macromolecule	Gap junction beta-2 protein (protein)

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5YC8 \| pdb_00005yc8	Download File View File

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS (Hg-derivative)

Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

Released	2018-11-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Muscarinic acetylcholine receptor M2,Redesigned apo-cytochrome b562,Muscarinic acetylcholine receptor M2 (protein)
Unique Ligands	3C0, HG

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5ZK3 \| pdb_00005zk3	Download File View File

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with QNB

Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

Released	2018-11-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2 (protein)
Unique Ligands	QNB

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5ZK8 \| pdb_00005zk8	Download File View File

Crystal structure of M2 muscarinic acetylcholine receptor bound with NMS

Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

Released	2018-11-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Muscarinic acetylcholine receptor M2,Redesigned apo-cytochrome b562,Muscarinic acetylcholine receptor M2 (protein)
Unique Ligands	3C0

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5ZKB \| pdb_00005zkb	Download File View File

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with AF-DX 384

Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

Released	2018-11-21
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Homo sapiens
Macromolecule	Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2 (protein)
Unique Ligands	82F

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5ZKC \| pdb_00005zkc	Download File View File

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS

Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

Released	2018-11-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2 (protein)
Unique Ligands	3C0

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6CRK \| pdb_00006crk	Download File View File

Heterotrimeric G-protein in complex with an antibody fragment

Maeda, S., Dawson, R., Kobilka, B.

(2018) Nat Commun 9: 3712-3712

Released	2018-10-24
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1 (protein) single-chain Fv (protein)
Unique Ligands	FLC, GDP

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6DDE \| pdb_00006dde	Download File View File

Mu Opioid Receptor-Gi Protein Complex

Koehl, A., Hu, H., Maeda, S., Manglik, A., Zhang, Y., Kobilka, B.K., Skiniotis, G., Weis, W.I.

(2018) Nature 558: 547-552

Released	2018-06-13
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6

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6DDF \| pdb_00006ddf	Download File View File

Mu Opioid Receptor-Gi Protein Complex

Koehl, A., Hu, H., Maeda, S., Manglik, A., Kobilka, B.K., Skiniotis, G., Weis, W.I.

(2018) Nature 558: 547-552

Released	2018-06-13
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	DAMGO (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1 (protein) Mu-type opioid receptor (protein)

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6OIJ \| pdb_00006oij	Download File View File

Muscarinic acetylcholine receptor 1-G11 protein complex

Maeda, S., Qianhui, Q., Skiniotis, G., Kobilka, B.

(2019) Science 364: 552-557

Released	2019-05-08
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Antibody fragment (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein subunit alpha-11 (protein) Muscarinic acetylcholine receptor M1 (protein)
Unique Ligands	IXO, Y01

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6OIK \| pdb_00006oik	Download File View File

Muscarinic acetylcholine receptor 2-Go complex

Maeda, S., Qianhui, Q., Skiniotis, G., Kobilka, B.

(2019) Science 364: 552-557

Released	2019-05-08
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Antibody fragment (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(o) subunit alpha (protein) Muscarinic acetylcholine receptor M2,Muscarinic acetylcholine receptor M2 (protein)
Unique Ligands	2CU, IXO

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6QNK \| pdb_00006qnk	Download File View File

Antibody FAB fragment targeting Gi protein heterotrimer

Tsai, C.-J., Muehle, J., Pamula, F., Dawson, R.J.P., Maeda, S., Deupi, X., Schertler, G.F.X.

(2019) Elife 8:

Released	2019-07-10
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Mus musculus
Macromolecule	FAB heavy chain (protein) FAB light chain (protein)
Unique Ligands	EDO, MLT, PG4, PGE

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6QNO \| pdb_00006qno	Download File View File

Rhodopsin-Gi protein complex

Tsai, C.-J., Marino, J., Adaixo, R.J., Pamula, F., Muehle, J., Maeda, S., Flock, T., Taylor, N.M.I., Mohammed, I., Matile, H., Dawson, R.J.P., Deupi, X., Stahlberg, H., Schertler, G.F.X.

(2019) Elife 8:

Released	2019-07-10
Method	ELECTRON MICROSCOPY 4.38 Å
Organisms	Bos taurus Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6
Unique Ligands	RET
Unique branched monosaccharides	NAG

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6WJC \| pdb_00006wjc	Download File View File

Muscarinic acetylcholine receptor 1 - muscarinic toxin 7 complex

Maeda, S., Kobilka, B.K.

(2020) Science 369: 161-167

Released	2020-07-08
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Dendroaspis angusticeps Homo sapiens Tequatrovirus T4
Macromolecule	Muscarinic acetylcholine receptor M1,Endolysin fusion (protein) Muscarinic toxin 7 (protein)
Unique Ligands	ACM, OIN, Y01

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7C4S \| pdb_00007c4s	Download File View File

Sphingosine-1-phosphate receptor 3 with a natural ligand.

Iwata, S., Maeda, S., Luo, F., Nango, E., hirata, K., Asada, H.

(2021) Sci Adv 7:

Released	2021-06-09
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Antibody Fab fragment heavy chain (protein) Antibody Fab fragment light chain (protein) Sphingosine 1-phosphate receptor 3 (protein)
Unique Ligands	S1P

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7JLO \| pdb_00007jlo	Download File View File

Cryo-EM structure of human ATG9A in amphipols

Maeda, S., Otomo, T.

(2020) Nat Struct Mol Biol 27: 1194-1201

Released	2020-10-28
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Autophagy-related protein 9A (protein)

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7JLP \| pdb_00007jlp	Download File View File

cryo-EM structure of human ATG9A in nanodiscs

Maeda, S., Otomo, T.

(2020) Nat Struct Mol Biol 27: 1194-1201

Released	2020-10-28
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Autophagy-related protein 9A (protein)
Unique Ligands	POV

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7JLQ \| pdb_00007jlq	Download File View File

cryo-EM structure of human ATG9A in LMNG micelles

Maeda, S., Otomo, T.

(2020) Nat Struct Mol Biol 27: 1194-1201

Released	2020-10-28
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens
Macromolecule	Autophagy-related protein 9A (protein)

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7RKF \| pdb_00007rkf	Download File View File

Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

Tsutsumi, N., Maeda, S., Qu, Q., Skiniotis, G., Kobilka, B.K., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

Released	2022-01-26
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens Human betaherpesvirus 5 Mus musculus
Macromolecule	Unique protein chains: 6
Unique Ligands	GDP, NAG

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7T5P \| pdb_00007t5p	Download File View File

Cryo-EM structure of human SIMC1-SLF2 complex

Maeda, S., Oravcova, M., Boddy, M.N., Otomo, T.

(2022) Elife 11:

Released	2022-12-07
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	SMC5-SMC6 complex localization factor protein 2 (protein) SUMO-interacting motif-containing protein 1 (protein)

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8UL9 \| pdb_00008ul9	Download File View File

Cholinephosphotransferase in complex with diacylglycerol

Roberts, J.R., Maeda, S., Ohi, M.D.

(2025) Nat Commun 16: 111-111

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cholinephosphotransferase 1 (protein)
Unique Ligands	DGA, MG, PCW

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8URP \| pdb_00008urp	Download File View File

Cholinephosphotransferase in complex with CDP-choline and phosphatidylcholine

Roberts, J.R., Maeda, S., Ohi, M.D.

(2025) Nat Commun 16: 111-111

Released	2024-10-30
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cholinephosphotransferase 1 (protein)
Unique Ligands	CDC, MG, PCF, PCW

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8URT \| pdb_00008urt	Download File View File

Cholinephosphotransferase in complex with selective inhibitor chelerythrine

Roberts, J.R., Maeda, S., Ohi, M.D.

(2025) Nat Commun 16: 111-111

Released	2024-10-30
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cholinephosphotransferase 1 (protein)
Unique Ligands	CTI, MG, PCW

1 to 23 of 23 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2ZW3 | pdb_00002zw3

5YC8 | pdb_00005yc8

5ZK3 | pdb_00005zk3

5ZK8 | pdb_00005zk8

5ZKB | pdb_00005zkb

5ZKC | pdb_00005zkc

6CRK | pdb_00006crk

6DDE | pdb_00006dde

6DDF | pdb_00006ddf

6OIJ | pdb_00006oij

6OIK | pdb_00006oik

6QNK | pdb_00006qnk

6QNO | pdb_00006qno

6WJC | pdb_00006wjc

7C4S | pdb_00007c4s

7JLO | pdb_00007jlo

7JLP | pdb_00007jlp

7JLQ | pdb_00007jlq

7RKF | pdb_00007rkf

7T5P | pdb_00007t5p

8UL9 | pdb_00008ul9

8URP | pdb_00008urp

8URT | pdb_00008urt