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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kawakami, K."

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Thermostichus vulcanus (5)
	Thermosynechococcus vestitus BP-1 (4)
	Acaryochloris marina MBIC11017 (1)
	Cyanidium caldarium (1)
	Gloeobacter violaceus PCC 7421 (1)
	Mus musculus (1)
	Nostoc sp. (1)

Taxonomy

	Bacteria (11)
	Eukaryota (2)

Experimental Method

	ELECTRON MICROSCOPY (8)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (3)
	2.5 - 3.0 (3)
	3.5 - 4.0 (2)
	4.0 - 4.5 (2)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (2)
	2015 - 2019 (1)
	2020 - 2024 (8)

Enzyme Classification Name

Oxidoreductases (10)

Membrane Protein Annotation

	PDBTM (7)
	mpstruc (6)
	MemProtMD (5)
	OPM (3)

Symmetry Type

	Asymmetric (6)
	Cyclic (6)
	Octahedral (1)

SCOP Classification

	Membrane and cell surface proteins and peptides (5)
	All alpha proteins (5)

AllSelected

1 to 13 of 13 Structures

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3A0B	Download File View File

Crystal structure of Br-substituted Photosystem II complex

Kawakami, K., Umena, Y., Kamiya, N., Shen, J.-R.

(2009) Proc Natl Acad Sci U S A 106: 8567-8572

Released	2009-05-19
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BR, CLA, DGD, FE2, HEM, LHG, MGE, OEC, PHO, PQ9

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3A0H	Download File View File

Crystal structure of I-substituted Photosystem II complex

Kawakami, K., Umena, Y., Kamiya, N., Shen, J.-R.

(2009) Proc Natl Acad Sci U S A 106: 8567-8572

Released	2009-05-19
Method	X-RAY DIFFRACTION 4 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, CLA, DGD, FE2, HEM, IOD, LHG, MGE, OEC, PHO, PQ9

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3WU2	Download File View File

Crystal structure analysis of Photosystem II complex

Umena, Y., Kawakami, K., Shen, J.R., Kamiya, N.

(2011) Nature 473: 55-60

Released	2014-09-03
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 19
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, FE2, GOL, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, RRX, SO4, SQD, UNL

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4IL6	Download File View File

Structure of Sr-substituted photosystem II

Koua, F.H.M., Umena, Y., Kawakami, K., Kamiya, N., Shen, J.R.

(2013) Proc Natl Acad Sci U S A 110: 3889-3894

Released	2013-03-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermostichus vulcanus Thermosynechococcus vestitus BP-1
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BCT, CL, CLA, DGD, DMS, FE2, GOL, HEM, HTG, LHG, LMG, LMT, MG, OER, PHO, PL9, SQD, UNL

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5H2F	Download File View File

Crystal structure of the PsbM-deletion mutant of photosystem II

Uto, S., Kawakami, K., Umena, Y., Iwai, M., Ikeuchi, M., Shen, J.R., Kamiya, N.

(2017) Faraday Discuss 198: 107-120

Released	2017-03-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	Unique protein chains: 18
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, DMS, FE2, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, RRX, SQD, UNL

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7COY	Download File View File

Structure of the far-red light utilizing photosystem I of Acaryochloris marina

Kawakami, K., Yonekura, K., Hamaguchi, T., Kashino, Y., Shinzawa-Itoh, K., Inoue-Kashino, N., Itoh, S., Ifuku, K., Yamashita, E.

(2021) Nat Commun 12: 2333-2333

Released	2021-03-31
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Acaryochloris marina MBIC11017
Macromolecule	Unique protein chains: 11
Unique Ligands	CL7, G9R, LHG, LMG, PHO, PQN, SF4, UNL

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7EDA	Download File View File

Structure of monomeric photosystem II

Yu, H., Hamaguchi, T., Nakajima, Y., Kato, K., kawakami, K., Akita, F., Yonekura, K., Shen, J.R.

(2021) Biochim Biophys Acta Bioenerg 1862: 148471-148471

Released	2021-07-07
Method	ELECTRON MICROSCOPY 2.78 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BCT, CLA, DGD, FE2, HEC, HEM, LHG, LMG, OEX, PHO, PL9, RRX, SQD, UNL

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7F4V	Download File View File

Cryo-EM structure of a primordial cyanobacterial photosystem I

Kato, K., Hamaguchi, T., Nagao, R., Kawakami, K., Yonekura, K., Shen, J.R.

(2022) bioRxiv

Released	2022-04-06
Method	ELECTRON MICROSCOPY 2.04 Å
Organisms	Gloeobacter violaceus PCC 7421
Macromolecule	Unique protein chains: 10
Unique Ligands	1L3, BCR, CL0, CLA, LHG, LMG, SF4

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7VEA	Download File View File

Pentacylindrical allophycocyanin core from Thermosynechococcus vulcanus

Kawakami, K., Hamaguchi, T., Hirose, Y., Kosumi, D., Miyata, M., Kamiya, N., Yonekura, K.

(2022) Nat Commun 13: 3389-3389

Released	2022-06-22
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	Allophycocyanin alpha chain (protein) Allophycocyanin beta chain (protein) Phycobiliprotein ApcE (protein) Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core (protein) Phycobilisome core component (protein)
Unique Ligands	CYC

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7VEB	Download File View File

Phycocyanin rod structure of cyanobacterial phycobilisome

Kawakami, K., Hamaguchi, T., Hirose, Y., Kosumi, D., Miyata, M., Kamiya, N., Yonekura, K.

(2022) Nat Commun 13: 3389-3389

Released	2022-06-15
Method	ELECTRON MICROSCOPY 4.2 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	C-phycocyanin alpha subunit (protein) C-phycocyanin beta subunit (protein) Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod (protein) Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod (protein) Phycobilisome rod-core linker polypeptide CpcG2 (protein)
Unique Ligands	CYC

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7Y3F	Download File View File

Structure of the Anabaena PSI-monomer-IsiA supercomplex

Nagao, R., Kato, K., Hamaguchi, T., Kawakami, K., Yonekura, K., Shen, J.R.

(2023) Nat Commun 14: 920-920

Released	2023-03-01
Method	ELECTRON MICROSCOPY 2.62 Å
Organisms	Nostoc sp.
Macromolecule	Unique protein chains: 14
Unique Ligands	BCR, CL0, CLA, LHG, LMG, LMT, PQN, SF4

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8J5A	Download File View File

Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)

Kawakami, K., Maki-Yonekura, S., Hamaguchi, T., Takaba, K., Yonekura, K.

(2023) Commun Chem 6: 98-98

Released	2023-07-12
Method	ELECTRON MICROSCOPY 1.19 Å
Organisms	Mus musculus
Macromolecule	Ferritin heavy chain (protein)
Unique Ligands	NA

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8WEY	Download File View File

PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)

Kato, K., Hamaguchi, T., Nakajima, Y., Kawakami, K., Yonekura, K., Shen, J.R., Nagao, R.

(2024) Proc Natl Acad Sci U S A 121: e2319658121-e2319658121

Released	2024-02-14
Method	ELECTRON MICROSCOPY 1.92 Å
Organisms	Cyanidium caldarium
Macromolecule	Unique protein chains: 15
Unique Ligands	5X6, BCR, CL0, CLA, DGD, LHG, LMT, PQN, SF4, UNL

1 to 13 of 13 Structures

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