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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kawakami, K."

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Search Summary

This query matches 41 Structures.

Refinements

Structure Determination Methodology

experimental (41)

Scientific Name of Source Organism

	Homo sapiens (22)
	Bos taurus (9)
	Mus musculus (9)
	Rattus norvegicus (7)
	unidentified (7)
	Thermostichus vulcanus (6)
	Thermosynechococcus vestitus BP-1 (4)
	Phytolacca americana (3)
	Cyanidium caldarium (2)
	Rattus rattus (2)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (12)
	unclassified sequences (7)

Experimental Method

	ELECTRON MICROSCOPY (29)
	X-RAY DIFFRACTION (12)

Polymer Entity Type

Protein (41)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (5)
	2.5 - 3.0 (14)
	3.0 - 3.5 (10)
	3.5 - 4.0 (4)
	4.0 - 4.5 (3)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (4)
	2015 - 2019 (3)
	2020 - 2024 (32)

Enzyme Classification Name

	Oxidoreductases (12)
	Hydrolases (17)
	Transferases (3)

Membrane Protein Annotation

	PDBTM (29)
	mpstruc (20)
	MemProtMD (15)
	OPM (15)

Symmetry Type

	Asymmetric (33)
	Cyclic (7)
	Octahedral (1)

SCOP Classification

	Membrane and cell surface proteins and peptides (6)
	All alpha proteins (6)
	Alpha and beta proteins (a/b) (3)
	All beta proteins (2)
	Alpha and beta proteins (a+b) (1)
	Artifacts (1)
	Small proteins (1)

AllSelected

1 to 25 of 41 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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3Q3K	Download File View File

Factor Xa in complex with a phenylenediamine derivative

Suzuki, M., Imai, E.

(2011) Bioorg Med Chem Lett 21: 2133-2140

Released	2011-12-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Activated factor Xa heavy chain (protein) Factor X light chain (protein)
Unique Ligands	CA, D90

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3T1F	Download File View File

Crystal structure of the mouse CD1d-Glc-DAG-s2 complex

Girardi, E., Zajonc, D.M.

(2011) Nat Immunol 12: 966-974

Released	2011-09-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus
Macromolecule	Antigen-presenting glycoprotein CD1d1 (protein) Beta-2-microglobulin (protein)
Unique Ligands	3TF, GOL, NAG
Unique branched monosaccharides	NAG

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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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4YUU	Download File View File

Crystal structure of oxygen-evolving photosystem II from a red alga

Ago, H., Shen, J.-R.

(2016) J Biol Chem 291: 5676-5687

Released	2016-01-20
Method	X-RAY DIFFRACTION 2.77000368116 Å
Organisms	Cyanidium caldarium
Macromolecule	Unique protein chains: 22
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, FE, GOL, HEM, LHG, LMG, LMT, OEX, 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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5V2C	Download File View File

RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX

Wang, J., Wiwczar, J.M., Brudvig, G.W.

(2017) Photosynth Res 134: 175-182

Released	2017-08-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 19
Unique Ligands	1PE, 2PE, BCR, BCT, CA, CL, CLA, DGD, EDO, FE2, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, P6G, PE8, PG4, PGE, PHO, PL9, SQD

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6JEL	Download File View File

Structure of Phytolacca americana apo UGT2

Maharjan, R., Fukuda, Y., Nakayama, T., Hamada, H., Ozaki, S., Inoue, T.

(2020) Biochemistry 59: 2551-2561

Released	2020-03-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Phytolacca americana
Macromolecule	Glycosyltransferase (protein)

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6JEM	Download File View File

Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and resveratrol

Maharjan, R., Fukuda, Y., Nakayama, T., Hamada, H., Ozaki, S., Inoue, T.

(2020) Biochemistry 59: 2551-2561

Released	2020-03-11
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Phytolacca americana
Macromolecule	Glycosyltransferase (protein)
Unique Ligands	STL, U2F

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6JEN	Download File View File

Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and pterostilbene

Maharjan, R., Fukuda, Y., Nakayama, T., Hamada, H., Ozaki, S., Inoue, T.

(2020) Biochemistry 59: 2551-2561

Released	2020-03-11
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Phytolacca americana
Macromolecule	Glycosyltransferase (protein)
Unique Ligands	3RL, U2F

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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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7EO2	Download File View File

Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to FTY720p

He, Y., Xu, Z., Ikuta, T.

(2022) Nat Chem Biol 18: 281-288

Released	2022-01-05
Method	ELECTRON MICROSCOPY 2.89 Å
Organisms	Homo sapiens
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) Sphingosine 1-phosphate receptor 1 (protein) scFv16 (protein)
Unique Ligands	J89

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7EO4	Download File View File

Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to BAF312

He, Y., Xu, Z., Ikuta, T., Inoue, A.

(2022) Nat Chem Biol 18: 281-288

Released	2022-01-05
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Homo sapiens
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) Sphingosine 1-phosphate receptor 1 (protein) scFv16 (protein)
Unique Ligands	J8C

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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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7VVJ	Download File View File

PTHrP-bound human PTH1R in complex with Gs

Kobayashi, K., Kusakizako, T., Miyauchi, H., Tomita, A., Kobayashi, K., Shihoya, W., Yamashita, K., Nishizawa, T., Kato, H.E., Nureki, O.

(2022) Mol Cell 82: 3468-3483.e5

Released	2022-08-03
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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7VVK	Download File View File

PTH-bound human PTH1R in complex with Gs (class1)

Kobayashi, K., Kusakizako, T., Miyauchi, H., Tomita, A., Kobayashi, K., Shihoya, W., Yamashita, K., Nishizawa, T., Kato, H.E., Nureki, O.

(2022) Mol Cell 82: 3468-3483.e5

Released	2022-08-03
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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7VVL	Download File View File

PTH-bound human PTH1R in complex with Gs (class2)

Kobayashi, K., Kusakizako, T., Miyauchi, H., Tomita, A., Kobayashi, K., Shihoya, W., Yamashita, K., Nishizawa, T., Kato, H.E., Nureki, O.

(2022) Mol Cell 82: 3468-3483.e5

Released	2022-08-03
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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7VVM	Download File View File

PTH-bound human PTH1R in complex with Gs (class3)

Kobayashi, K., Kusakizako, T., Miyauchi, H., Tomita, A., Kobayashi, K., Shihoya, W., Yamashita, K., Nishizawa, T., Kato, H.E., Nureki, O.

(2022) Mol Cell 82: 3468-3483.e5

Released	2022-08-03
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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7VVN	Download File View File

PTH-bound human PTH1R in complex with Gs (class4)

Kobayashi, K., Kusakizako, T., Miyauchi, H., Tomita, A., Kobayashi, K., Shihoya, W., Yamashita, K., Nishizawa, T., Kato, H.E., Nureki, O.

(2022) Mol Cell 82: 3468-3483.e5

Released	2022-08-03
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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7VVO	Download File View File

PTH-bound human PTH1R in complex with Gs (class5)

Kobayashi, K., Kusakizako, T., Miyauchi, H., Tomita, A., Kobayashi, K., Shihoya, W., Yamashita, K., Nishizawa, T., Kato, H.E., Nureki, O.

(2022) Mol Cell 82: 3468-3483.e5

Released	2022-08-03
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

1 to 25 of 41 Structures

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