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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Fujii, Y."

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Search Summary

This query matches 28 Structures.

Refinements

Structure Determination Methodology

experimental (28)

Scientific Name of Source Organism

	Homo sapiens (13)
	Pseudonocardia autotrophica (5)
	Mus musculus (4)
	Paenibacillus sp. FPU-7 (3)
	Rattus norvegicus (2)
	Influenza A virus (A/Aichi/2-1/1968(H3N2)) (1)
	Irpex lacteus (1)
	Nonomuraea recticatena (1)
	Protobothrops flavoviridis (1)
	Schizosaccharomyces pombe (1)

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Taxonomy

	Eukaryota (18)
	Bacteria (11)
	Riboviria (1)

Experimental Method

X-RAY DIFFRACTION (28)

Polymer Entity Type

	Protein (28)
	DNA (10)

Refinement Resolution (Å)

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

Release Date

	1995 - 1999 (1)
	2000 - 2004 (3)
	2005 - 2009 (1)
	2010 - 2014 (6)
	2015 - 2019 (14)
	2020 - 2024 (3)

Enzyme Classification Name

	Oxidoreductases (6)
	Hydrolases (4)

Membrane Protein Annotation

	MemProtMD (3)
	PDBTM (3)
	mpstruc (3)
	OPM (2)

Symmetry Type

	Asymmetric (19)
	Cyclic (11)

SCOP Classification

	All alpha proteins (9)
	All beta proteins (5)
	Coiled coil proteins (1)
	Artifacts (1)
	Small proteins (1)

AllSelected

1 to 25 of 28 Structures

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1GD2 \| pdb_00001gd2	Download File View File

CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA

Fujii, Y., Shimizu, T., Toda, T., Yanagida, M., Hakoshima, T.

(2000) Nat Struct Biol 7: 889-893

Released	2000-10-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	TRANSCRIPTION FACTOR PAP1 (protein) DNA (5'-D(APGPGPTPTPAPCPGPTPAPAPCP*C)-3') (nucleic acid)

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1J2L \| pdb_00001j2l	Download File View File

Crystal structure of the disintegrin, trimestatin

Fujii, Y., Okuda, D., Fujimoto, Z., Morita, T., Mizuno, H.

(2003) J Mol Biology 332: 1115-1122

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Protobothrops flavoviridis
Macromolecule	Disintegrin triflavin (protein)
Unique Ligands	SO4

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1WKR \| pdb_00001wkr	Download File View File

Crystal structure of aspartic proteinase from Irpex lacteus

Fujimoto, Z., Fujii, Y., Kaneko, S., Kobayashi, H., Mizuno, H.

(2004) J Mol Biology 341: 1227-1235

Released	2004-09-07
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Irpex lacteus Streptomyces argenteolus subsp. toyonakensis
Macromolecule	Polyporopepsin (protein) pepstatin (protein)
Unique Ligands	SO4

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2IRF \| pdb_00002irf	Download File View File

CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX.

Fujii, Y., Shimizu, T., Kusumoto, M., Kyogoku, Y., Taniguchi, T., Hakoshima, T.

(1999) EMBO J 18: 5028-5041

Released	1999-10-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mus musculus
Macromolecule	INTERFERON REGULATORY FACTOR 2 (protein) DNA (5'-D(TPTPCPAPCPTPTPTPCPAPCP(5IU)PT)-3') (nucleic acid) DNA (5'-D(PAPAPGPTPGPAPAPAPGP(5IU)PGP*A)-3') (nucleic acid)
Unique Ligands	K

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2Z36 \| pdb_00002z36	Download File View File

Crystal structure of cytochrome P450 MoxA from Nonomuraea recticatena (CYP105)

Yasutake, Y., Fujii, Y., Fujii, T., Arisawa, A., Tamura, T.

(2007) Biochem Biophys Res Commun 361: 876-882

Released	2007-08-21
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Nonomuraea recticatena
Macromolecule	Cytochrome P450 type compactin 3'',4''-hydroxylase (protein)
Unique Ligands	FE, HEM, MES

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3A4G \| pdb_00003a4g	Download File View File

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form)

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-14
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	HEM, PG0

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3A4H \| pdb_00003a4h	Download File View File

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-14
Method	X-RAY DIFFRACTION 3.06 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	CA, HEM

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3A4Z \| pdb_00003a4z	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM

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3A50 \| pdb_00003a50	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound vitamin D3

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM, VD3

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3A51 \| pdb_00003a51	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin D3

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM, VDY

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3WHE \| pdb_00003whe	Download File View File

A new conserved neutralizing epitope at the globular head of hemagglutinin in H3N2 influenza viruses

Fujii, Y., Sumida, T., Shirouzu, M., Yokoyama, S.

(2014) J Virol 88: 7130-7144

Released	2014-04-23
Method	X-RAY DIFFRACTION 4 Å
Organisms	Homo sapiens Influenza A virus (A/Aichi/2-1/1968(H3N2))
Macromolecule	Hemagglutinin (protein) immunoglobulin heavy chain (protein) immunoglobulin light chain (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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4YNY \| pdb_00004yny	Download File View File

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1

Fujii, Y., Kitago, Y., Arimori, T., Takagi, J.

(2016) J Cell Sci 129: 1512-1522

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.584 Å
Organisms	Rattus norvegicus
Macromolecule	Heavy chain of antigen binding fragment, Fab (protein) Light chain of antigen binding fragment, Fab (protein)

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4YO0 \| pdb_00004yo0	Download File View File

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide

Fujii, Y., Kitago, Y., Arimori, T., Takagi, J.

(2016) J Cell Sci 129: 1512-1522

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Heavy chain of antigen binding fragment, Fab (protein) Light chain of antigen binding fragment, Fab (protein) PA14 peptide (protein)
Unique Ligands	EDO

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5AV5 \| pdb_00005av5	Download File View File

human nucleosome core particle

Wakamori, M., Fujii, Y., Umehara, T., Yokoyama, S.

(2015) Sci Rep 5: 17204-17204

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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5AV6 \| pdb_00005av6	Download File View File

human nucleosome core particle

Wakamori, M., Fujii, Y., Umehara, T., Yokoyama, S.

(2015) Sci Rep 5: 17204-17204

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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5AV8 \| pdb_00005av8	Download File View File

human nucleosome core particle

Wakamori, M., Fujii, Y., Umehara, T., Yokoyama, S.

(2015) Sci Rep 5: 17204-17204

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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5AV9 \| pdb_00005av9	Download File View File

human nucleosome core particle

Wakamori, M., Fujii, Y., Umehara, T., Yokoyama, S.

(2015) Sci Rep 5: 17204-17204

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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5AVB \| pdb_00005avb	Download File View File

human nucleosome core particle

Wakamori, M., Fujii, Y., Umehara, T., Yokoyama, S.

(2015) Sci Rep 5: 17204-17204

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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5AVC \| pdb_00005avc	Download File View File

human nucleosome core particle

Wakamori, M., Fujii, Y., Umehara, T., Yokoyama, S.

(2015) Sci Rep 5: 17204-17204

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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5B2I \| pdb_00005b2i	Download File View File

Human nucleosome containing CpG unmethylated DNA

Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S.

(2016) FEBS Open Bio 6: 498-514

Released	2016-06-15
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Histone H2A type 1-B/E (protein) Histone H2B type 1-J (protein) Histone H3.1 (protein) Histone H4 (protein) DNA (146-MER) (nucleic acid)
Unique Ligands	MN

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5B2J \| pdb_00005b2j	Download File View File

Human nucleosome containing CpG methylated DNA

Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S.

(2016) FEBS Open Bio 6: 498-514

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Histone H2A type 1-B/E (protein) Histone H2B type 1-J (protein) Histone H3.1 (protein) Histone H4 (protein) DNA (146-MER) (nucleic acid)
Unique Ligands	MN

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5GZT \| pdb_00005gzt	Download File View File

Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery

Itoh, T., Hibi, T., Suzuki, F., Sugimoto, I., Fujiwara, A., Inaka, K., Tanaka, H., Ohta, K., Fujii, Y., Taketo, A., Kimoto, H.

(2016) PLoS One 11: e0167310-e0167310

Released	2016-12-28
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Paenibacillus sp. FPU-7
Macromolecule	Chitinase (protein)
Unique Ligands	FMT, NA, PO4

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5GZU \| pdb_00005gzu	Download File View File

Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery

Itoh, T., Hibi, T., Suzuki, F., Sugimoto, I., Fujiwara, A., Inaka, K., Tanaka, H., Ohta, K., Fujii, Y., Taketo, A., Kimoto, H.

(2016) PLoS One 11: e0167310-e0167310

Released	2016-12-28
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Paenibacillus sp. FPU-7
Macromolecule	Chitinase (protein)
Unique Ligands	PO4

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5GZV \| pdb_00005gzv	Download File View File

Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery

Itoh, T., Hibi, T., Suzuki, F., Sugimoto, I., Fujiwara, A., Inaka, K., Tanaka, H., Ohta, K., Fujii, Y., Taketo, A., Kimoto, H.

(2016) PLoS One 11: e0167310-e0167310

Released	2016-12-28
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Paenibacillus sp. FPU-7
Macromolecule	Chitinase (protein)
Unique Ligands	PO4
Unique branched monosaccharides	NAG