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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Caesar, J."

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Search Summary

This query matches 33 Structures.

Refinements

Structure Determination Methodology

experimental (33)

Scientific Name of Source Organism

	Homo sapiens (9)
	Trichodesmium erythraeum IMS101 (4)
	synthetic construct (3)
	Achromobacter cycloclastes (2)
	Aquifex aeolicus VF5 (2)
	Leptolyngbya sp. O-77 (2)
	Mus musculus (2)
	Pseudomonas fluorescens (2)
	Saccharomyces cerevisiae (2)
	Aquifex aeolicus (1)

More...

Taxonomy

	Bacteria (17)
	Eukaryota (13)
	other sequences (3)
	Archaea (2)

Experimental Method

	ELECTRON MICROSCOPY (29)
	X-RAY DIFFRACTION (4)

Polymer Entity Type

	Protein (33)
	RNA (2)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (4)
	2.5 - 3.0 (13)
	3.0 - 3.5 (10)
	3.5 - 4.0 (5)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (2)
	2010 - 2014 (1)
	2020 - 2024 (29)

Enzyme Classification Name

	Ligases (4)
	Hydrolases (4)
	Transferases (2)
	Translocases (2)
	Lyases (2)
	Oxidoreductases (3)

Membrane Protein Annotation

	PDBTM (7)
	mpstruc (2)
	MemProtMD (1)
	OPM (1)

Symmetry Type

	Cyclic (14)
	Dihedral (10)
	Asymmetric (7)
	Helical (1)
	Icosahedral (1)
	Octahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (2)
	All beta proteins (3)
	Artifacts (2)

AllSelected

1 to 25 of 33 Structures

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1IXV \| pdb_00001ixv	Download File View File

Crystal Structure Analysis of homolog of oncoprotein gankyrin, an interactor of Rb and CDK4/6

Padmanabhan, B., Adachi, N., Kataoka, K., Horikoshi, M.

(2004) J Biological Chem 279: 1546-1552

Released	2003-12-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Probable 26S proteasome regulatory subunit p28 (protein)

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1WG3 \| pdb_00001wg3	Download File View File

Structural analysis of yeast nucleosome-assembly factor CIA1p

Padmanabhan, B., Kataoka, K., Umehara, T., Adachi, N., Yokoyama, S., Horikoshi, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Biochem 138: 821-829

Released	2005-06-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Anti-silencing protein 1 (protein)

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2Z8U \| pdb_00002z8u	Download File View File

Methanococcus jannaschii TBP

Adachi, N., Senda, T., Horikoshi, M.

(2008) Genes Cells 13: 1127-1140

Released	2008-08-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	TATA-box-binding protein (protein)

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3AAD \| pdb_00003aad	Download File View File

Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction

Akai, Y., Adachi, N., Hayashi, Y., Eitoku, M., Sano, N., Natsume, R., Kudo, N., Tanokura, M., Senda, T., Horikoshi, M.

(2010) Proc Natl Acad Sci U S A 107: 8153-8158

Released	2010-04-28
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Histone chaperone ASF1A (protein) Transcription initiation factor TFIID subunit 1 (protein)
Unique Ligands	SO4

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6KNF \| pdb_00006knf	Download File View File

CryoEM map and model of Nitrite Reductase at pH 6.2

Adachi, N., Yamaguchi, T., Moriya, T., Kawasaki, M., Koiwai, K., Shinoda, A., Yamada, Y., Yumoto, F., Kohzuma, T., Senda, T.

(2021) J Struct Biol 213: 107768-107768

Released	2020-08-12
Method	ELECTRON MICROSCOPY 2.99 Å
Organisms	Achromobacter cycloclastes
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU

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6KNG \| pdb_00006kng	Download File View File

CryoEM map and model of Nitrite Reductase at pH 8.1

Adachi, N., Yamaguchi, T., Moriya, T., Kawasaki, M., Koiwai, K., Shinoda, A., Yamada, Y., Yumoto, F., Kohzuma, T., Senda, T.

(2021) J Struct Biol 213: 107768-107768

Released	2020-08-12
Method	ELECTRON MICROSCOPY 2.85 Å
Organisms	Achromobacter cycloclastes
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU

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6M3X \| pdb_00006m3x	Download File View File

Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii

Sato, Y., Adachi, N., Moriya, T., Arakawa, T., Kawasaki, M., Yamada, C., Senda, T., Fushinobu, S.

(2020) J Struct Biol X 4: 100030-100030

Released	2020-07-15
Method	ELECTRON MICROSCOPY 2.24 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	Sulfur oxygenase/reductase (protein)
Unique Ligands	FE

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7CN0 \| pdb_00007cn0	Download File View File

Cryo-EM structure of K+-bound hERG channel

Asai, T., Adachi, N., Moriya, T., Kawasaki, M., Suzuki, K., Senda, T., Murata, T.

(2021) Structure 29: 203-212.e4

Released	2021-01-20
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens
Macromolecule	potassium channel 1 (protein)
Unique Ligands	K

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7CN1 \| pdb_00007cn1	Download File View File

Cryo-EM structure of K+-bound hERG channel in the presence of astemizole

Asai, T., Adachi, N., Moriya, T., Kawasaki, M., Suzuki, K., Senda, T., Murata, T.

(2021) Structure 29: 203-212.e4

Released	2021-01-20
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Homo sapiens
Macromolecule	potassium channel (protein)
Unique Ligands	K

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7DRD \| pdb_00007drd	Download File View File

Cryo-EM structure of DgpB-C at 2.85 angstrom resolution

Mori, T., Moriya, T., Adachi, N., Senda, T., Abe, I.

(2021) Nat Commun 12: 6294-6294

Released	2021-12-08
Method	ELECTRON MICROSCOPY 2.85 Å
Organisms	human intestinal bacterium PUE
Macromolecule	AP_endonuc_2 domain-containing protein (protein) DgpB (protein)

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7DRE \| pdb_00007dre	Download File View File

Cryo-EM structure of DfgA-B at 2.54 angstrom resolution

Mori, T., Moriya, T., Adachi, N., Senda, T., Abe, I.

(2021) Nat Commun 12: 6294-6294

Released	2021-12-08
Method	ELECTRON MICROSCOPY 2.54 Å
Organisms	[Eubacterium] cellulosolvens 6
Macromolecule	DfgB (protein) Sugar phosphate isomerase/epimerase (protein)

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7EH7 \| pdb_00007eh7	Download File View File

Cryo-EM structure of the octameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77

Minato, T., Teramoto, T., Adachi, N., Hung, N.K., Yamada, K., Kawasaki, M., Akutsu, M., Moriya, T., Senda, T., Ogo, S., Kakuta, Y., Yoon, K.S.

(2021) Commun Biol 4: 1238-1238

Released	2021-11-17
Method	ELECTRON MICROSCOPY 3.71 Å
Organisms	Leptolyngbya sp. O-77
Macromolecule	C-phycocyanin alpha chain (protein) C-phycocyanin beta chain (protein)
Unique Ligands	CYC

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7EH8 \| pdb_00007eh8	Download File View File

Cryo-EM structure of the hexameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77

Minato, T., Teramoto, T., Adachi, N., Hung, N.K., Yamada, K., Kawasaki, M., Akutsu, M., Moriya, T., Senda, T., Ogo, S., Kakuta, Y., Yoon, K.S.

(2021) Commun Biol 4: 1238-1238

Released	2021-11-17
Method	ELECTRON MICROSCOPY 3.06 Å
Organisms	Leptolyngbya sp. O-77
Macromolecule	C-phycocyanin alpha chain (protein) C-phycocyanin beta chain (protein)
Unique Ligands	CYC

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7F3E \| pdb_00007f3e	Download File View File

Cryo-EM structure of the minimal protein-only RNase P from Aquifex aeolicus

Teramoto, T., Koyasu, T., Adachi, N., Kawasaki, M., Moriya, T., Numata, T., Senda, T., Kakuta, Y.

(2021) J Biological Chem 297: 101028-101028

Released	2021-08-11
Method	ELECTRON MICROSCOPY 3.62 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	RNA-free ribonuclease P (protein)

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7WAC \| pdb_00007wac	Download File View File

Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1)

Kawasaki, M., Miyakawa, T., Yang, J., Adachi, N., Fujii, A., Miyauchi, Y., Muramatsu, T., Moriya, T., Senda, T., Tanokura, M.

(2022) Nat Commun 13: 5097-5097

Released	2022-09-07
Method	ELECTRON MICROSCOPY 2.91 Å
Organisms	Trichodesmium erythraeum IMS101
Macromolecule	Cyanophycin synthase (protein)

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7WAD \| pdb_00007wad	Download File View File

Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS

Kawasaki, M., Miyakawa, T., Yang, J., Adachi, N., Fujii, A., Miyauchi, Y., Muramatsu, T., Moriya, T., Senda, T., Tanokura, M.

(2022) Nat Commun 13: 5097-5097

Released	2022-09-07
Method	ELECTRON MICROSCOPY 2.96 Å
Organisms	Trichodesmium erythraeum IMS101
Macromolecule	Cyanophycin synthase (protein)
Unique Ligands	AGS, MG

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7WAE \| pdb_00007wae	Download File View File

Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS, 4x(beta-Asp-Arg), and aspartate

Miyakawa, T., Yang, J., Kawasaki, M., Adachi, N., Fujii, A., Miyauchi, Y., Muramatsu, T., Moriya, T., Senda, T., Tanokura, M.

(2022) Nat Commun 13: 5097-5097

Released	2022-09-07
Method	ELECTRON MICROSCOPY 2.64 Å
Organisms	Trichodesmium erythraeum IMS101 synthetic construct
Macromolecule	4x(beta-Asp-Arg) (protein) Cyanophycin synthase (protein)
Unique Ligands	AGS, ARG, ASP, MG

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7WAF \| pdb_00007waf	Download File View File

Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS and 4x(beta-Asp-Arg)

Miyakawa, T., Yang, J., Kawasaki, M., Adachi, N., Fujii, A., Miyauchi, Y., Muramatsu, T., Moriya, T., Senda, T., Tanokura, M.

(2022) Nat Commun 13: 5097-5097

Released	2022-09-07
Method	ELECTRON MICROSCOPY 2.52 Å
Organisms	Trichodesmium erythraeum IMS101 synthetic construct
Macromolecule	4x(beta-Asp-Arg) (protein) Cyanophycin synthase (protein)
Unique Ligands	AGS, ARG, MG

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7WIJ \| pdb_00007wij	Download File View File

Cryo-EM structure of prenyltransferase domain of Macrophoma phaseolina macrophomene synthase

Mori, T., Adachi, N., Abe, I.

(2022) Nature 606: 414-419

Released	2022-06-22
Method	ELECTRON MICROSCOPY 3.17 Å
Organisms	Macrophomina phaseolina MS6
Macromolecule	Geranylgeranyl diphosphate synthase (protein)

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7WLG \| pdb_00007wlg	Download File View File

Cryo-EM structure of GH31 alpha-1,3-glucosidase from Lactococcus lactis subsp. cremoris

Ikegaya, M., Moriya, T., Adachi, N., Kawasaki, M., Park, E.Y., Miyazaki, T.

(2022) J Biological Chem 298: 101827-101827

Released	2022-03-30
Method	ELECTRON MICROSCOPY 2.73 Å
Organisms	Lactococcus cremoris subsp. cremoris MG1363
Macromolecule	Alpha-xylosidase (protein)

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7XM1 \| pdb_00007xm1	Download File View File

Cryo-EM structure of mTIP60-Ba (metal-ion induced TIP60 (K67E) complex with barium ions

Ohara, N., Kawakami, N., Arai, R., Adachi, N., Moriya, T., Kawasaki, M., Miyamoto, K.

(2023) J Am Chem Soc 145: 216-223

Released	2023-01-04
Method	ELECTRON MICROSCOPY 3.96 Å
Organisms	synthetic construct
Macromolecule	TIP60 K67E mutant (protein)
Unique Ligands	BA

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8HW1 \| pdb_00008hw1	Download File View File

Far-red light-harvesting complex of Antarctic alga Prasiola crispa

Kosugi, M., Kawasaki, M., Shibata, Y., Moriya, T., Adachi, N., Senda, T.

(2023) Nat Commun 14: 730-730

Released	2023-01-18
Method	ELECTRON MICROSCOPY 3.13 Å
Organisms	Prasiola crispa
Macromolecule	Far-red light-harvesting complex (protein)
Unique Ligands	32N, CLA, XAT

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8K3H \| pdb_00008k3h	Download File View File

Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution

Mori, T., Awakawa, T., Adachi, N., Abe, I.

To be published

Released	2024-07-17
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Pseudomonas fluorescens
Macromolecule	PseP (protein)
Unique Ligands	NAD

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8K3I \| pdb_00008k3i	Download File View File

Cryo-EM structure of PseP apo

Mori, T., Awakawa, T., Adachi, N., Abe, I.

To be published

Released	2024-07-17
Method	ELECTRON MICROSCOPY 2.83 Å
Organisms	Pseudomonas fluorescens
Macromolecule	PseP (protein)

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8KD9 \| pdb_00008kd9	Download File View File

Cryo-EM structure of Aquifex aeolicus minimal protein-only RNase P (HARP) in complex with pre-tRNAs

Teramoto, T., Koyasu, T., Mayanagi, K., Yokogawa, T., Adachi, N., Nakamura, T., Senda, T., Kakuta, Y.

To be published

Released	2024-08-14
Method	ELECTRON MICROSCOPY 2.87 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	RNA-free ribonuclease P (protein) Aquifex aeolicus pre-tRNAVal (nucleic acid)

1 to 25 of 33 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

1IXV | pdb_00001ixv

1WG3 | pdb_00001wg3

2Z8U | pdb_00002z8u

3AAD | pdb_00003aad

6KNF | pdb_00006knf

6KNG | pdb_00006kng

6M3X | pdb_00006m3x

7CN0 | pdb_00007cn0

7CN1 | pdb_00007cn1

7DRD | pdb_00007drd

7DRE | pdb_00007dre

7EH7 | pdb_00007eh7

7EH8 | pdb_00007eh8

7F3E | pdb_00007f3e

7WAC | pdb_00007wac

7WAD | pdb_00007wad

7WAE | pdb_00007wae

7WAF | pdb_00007waf

7WIJ | pdb_00007wij

7WLG | pdb_00007wlg

7XM1 | pdb_00007xm1

8HW1 | pdb_00008hw1

8K3H | pdb_00008k3h

8K3I | pdb_00008k3i

8KD9 | pdb_00008kd9