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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yajima, H."

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Search Summary

This query matches 37 Structures.

Refinements

Structure Determination Methodology

experimental (37)

Scientific Name of Source Organism

	Homo sapiens (10)
	Trypanosoma cruzi (6)
	Saccharomyces cerevisiae S288C (5)
	Pyrococcus furiosus (4)
	Shewanella oneidensis MR-1 (3)
	Arabidopsis thaliana (2)
	Kluyveromyces marxianus (2)
	Mus musculus (2)
	Bos taurus (1)
	Neospora caninum (1)

More...

Taxonomy

	Eukaryota (29)
	Archaea (4)
	Bacteria (4)

Experimental Method

	X-RAY DIFFRACTION (32)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

Protein (37)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (13)
	2.5 - 3.0 (6)
	3.0 - 3.5 (8)
	3.5 - 4.0 (2)
	4.0 - 4.5 (1)
	> 4.5 (2)

Release Date

	2005 - 2009 (4)
	2010 - 2014 (6)
	2015 - 2019 (9)
	2020 - 2024 (18)

Enzyme Classification Name

	Hydrolases (10)
	Transferases (8)
	Isomerases (4)

Membrane Protein Annotation

	MemProtMD (4)
	PDBTM (4)
	mpstruc (4)
	OPM (3)

Symmetry Type

	Asymmetric (21)
	Cyclic (19)
	Dihedral (2)
	Tetrahedral (2)

SCOP Classification

	Alpha and beta proteins (a/b) (7)
	Artifacts (10)
	Alpha and beta proteins (a+b) (4)
	All alpha proteins (1)
	All beta proteins (1)

AllSelected

1 to 25 of 37 Structures

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2ZJ2 \| pdb_00002zj2	Download File View File

Archaeal DNA helicase Hjm apo state in form 1

Oyama, T., Oka, H., Fujikane, R., Ishino, Y., Morikawa, K.

(2009) BMC Struct Biol 9: 2-2

Released	2009-02-10
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative ski2-type helicase (protein)
Unique Ligands	SO4

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2ZJ5 \| pdb_00002zj5	Download File View File

Archaeal DNA helicase Hjm complexed with ADP in form 1

Oyama, T., Oka, H., Fujikane, R., Ishino, Y., Morikawa, K.

(2009) BMC Struct Biol 9: 2-2

Released	2009-02-10
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative ski2-type helicase (protein)
Unique Ligands	ADP, SO4

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2ZJ8 \| pdb_00002zj8	Download File View File

Archaeal DNA helicase Hjm apo state in form 2

Oyama, T., Oka, H., Fujikane, R., Ishino, Y., Morikawa, K.

(2009) BMC Struct Biol 9: 2-2

Released	2009-02-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative ski2-type helicase (protein)

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2ZJA \| pdb_00002zja	Download File View File

Archaeal DNA helicase Hjm complexed with AMPPCP in form 2

Oyama, T., Oka, H., Fujikane, R., Ishino, Y., Morikawa, K.

(2009) BMC Struct Biol 9: 2-2

Released	2009-02-10
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative ski2-type helicase (protein)
Unique Ligands	ACP

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3AGR \| pdb_00003agr	Download File View File

Crystal structure of nucleoside triphosphate hydrolases from Neospora caninum

Matoba, K., Shiba, T., Seiki, M., Asai, T., Harada, S.

To be published

Released	2011-04-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Neospora caninum
Macromolecule	Nucleoside triphosphate hydrolase (protein)

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3VI1 \| pdb_00003vi1	Download File View File

Crystal structure of Pseudomonas aerginosa alkaline protease complexed with Substance P(1-6)

Matoba, K., Harada, S.

To be published

Released	2012-09-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Alkaline metalloproteinase (protein) Substance P1-6, RPKPQQ (protein)
Unique Ligands	CA, ZN

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3VKF \| pdb_00003vkf	Download File View File

Crystal Structure of Neurexin 1beta/Neuroligin 1 complex

Tanaka, H., Miyazaki, N., Nogi, T., Iwasaki, K., Takagi, J.

(2012) Cell Rep 2: 101-110

Released	2012-08-01
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Bos taurus Rattus norvegicus
Macromolecule	Neurexin-1-beta (protein) Neuroligin-1 (protein)
Unique Ligands	CA, NAG
Unique branched monosaccharides	BMA, NAG

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3VX6 \| pdb_00003vx6	Download File View File

Crystal structure of Kluyveromyces marxianus Atg7NTD

Yamaguchi, M., Matoba, K., Sawada, R., Fujioka, Y., Nakatogawa, H., Yamamoto, H., Kobashigawa, Y., Hoshida, H., Akada, R., Ohsumi, Y., Noda, N.N., Inagaki, F.

(2012) Nat Struct Mol Biol 19: 1250-1256

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Kluyveromyces marxianus
Macromolecule	E1 (protein)

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3VX7 \| pdb_00003vx7	Download File View File

Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex

Yamaguchi, M., Matoba, K., Sawada, R., Fujioka, Y., Nakatogawa, H., Yamamoto, H., Kobashigawa, Y., Hoshida, H., Akada, R., Ohsumi, Y., Noda, N.N., Inagaki, F.

(2012) Nat Struct Mol Biol 19: 1250-1256

Released	2012-11-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Kluyveromyces marxianus
Macromolecule	E1 (protein) E2 (protein)

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3VX8 \| pdb_00003vx8	Download File View File

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex

Matoba, K., Fujioka, Y., Noda, N.N.

(2012) Nat Struct Mol Biol 19: 1250-1256

Released	2012-11-14
Method	X-RAY DIFFRACTION 3.11 Å
Organisms	Arabidopsis thaliana
Macromolecule	Autophagy-related protein 3 (protein) Ubiquitin-like modifier-activating enzyme atg7 (protein)

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5GJE \| pdb_00005gje	Download File View File

Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1

Matoba, K., Mihara, E., Tamura-Kawakami, K., Hirai, H., Thompson, S., Iwasaki, K., Takagi, J.

(2017) Cell Rep 18: 32-40

Released	2017-01-18
Method	ELECTRON MICROSCOPY 21 Å
Organisms	Homo sapiens
Macromolecule	Dickkopf-related protein 1 (protein) Low-density lipoprotein receptor-related protein 6 (protein)
Unique Ligands	GOL, NAG, PO4
Unique branched monosaccharides	FUC, NAG

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5JGE \| pdb_00005jge	Download File View File

Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide

Watanabe, Y., Noda, N.N.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C
Macromolecule	Ape1 propeptide (protein) Autophagy-related protein 19 (protein)

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5JGF \| pdb_00005jgf	Download File View File

Crystal structure of mApe1

Noda, N.N., Adachi, W., Inagaki, F.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)
Unique Ligands	ZN

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5JH9 \| pdb_00005jh9	Download File View File

Crystal structure of prApe1

Noda, N.N., Adachi, W., Inagaki, F.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)
Unique Ligands	CAC, ZN

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5JHC \| pdb_00005jhc	Download File View File

Crystal structure of the self-assembled propeptides from Ape1

Yamasaki, A., Noda, N.N.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)

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6AHY \| pdb_00006ahy	Download File View File

Wnt signaling complex

Hirai, H., Arimori, T., Matoba, K., Mihara, E., Takagi, J.

(2019) Nat Struct Mol Biol 26: 372-379

Released	2019-05-01
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Frizzled-8 (protein) Proto-oncogene Wnt-3 (protein)
Unique Ligands	CL, NAG, PAM
Unique branched monosaccharides	NAG

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6JI1 \| pdb_00006ji1	Download File View File

Tetrameric PepTSo2 incorporated in salipro nano particle

Kawamoto, A., Matoba, K., Takagi, J.

(2019) Acta Crystallogr F Struct Biol Commun 75: 348-358

Released	2019-05-15
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Shewanella oneidensis MR-1
Macromolecule	Proton:oligopeptide symporter POT family (protein)

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6JKC \| pdb_00006jkc	Download File View File

Crystal structure of tetrameric PepTSo2 in P4212 space group

Nagamura, R., Fukuda, M., Ishitani, R., Nureki, O.

(2019) Acta Crystallogr F Struct Biol Commun 75: 348-358

Released	2019-05-15
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Shewanella oneidensis MR-1
Macromolecule	Proton:oligopeptide symporter POT family (protein)

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6JKD \| pdb_00006jkd	Download File View File

Crystal structure of tetrameric PepTSo2 in I4 space group

Nagamura, R., Fukuda, M., Ishitani, R., Nureki, O.

(2019) Acta Crystallogr F Struct Biol Commun 75: 348-358

Released	2019-05-15
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Shewanella oneidensis MR-1
Macromolecule	Proton:oligopeptide symporter POT family (protein)

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6JKQ \| pdb_00006jkq	Download File View File

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi (Ligand-free form)

Matoba, K., Shiba, T., Nara, T., Aoki, T., Nagasaki, S., Hayamizu, R., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Balogun, E.O., Inaoka, D.K., Kita, K., Harada, S.

To be published

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Trypanosoma cruzi
Macromolecule	Aspartate carbamoyltransferase (protein)

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6JKR \| pdb_00006jkr	Download File View File

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl phosphate (CP)

Matoba, K., Shiba, T., Nara, T., Aoki, T., Nagasaki, S., Hayamizu, R., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Balogun, E.O., Inaoka, D.K., Kita, K., Harada, S.

To be published

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Trypanosoma cruzi
Macromolecule	Aspartate carbamoyltransferase (protein)
Unique Ligands	CP, GOL

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6JKS \| pdb_00006jks	Download File View File

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl phosphate (CP) and aspartate (Asp)

Matoba, K., Shiba, T., Nara, T., Aoki, T., Nagasaki, S., Hayamizu, R., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Balogun, E.O., Inaoka, D.K., Kita, K., Harada, S.

To be published

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Trypanosoma cruzi strain CL Brener
Macromolecule	Aspartate carbamoyltransferase, putative (protein)
Unique Ligands	ASP, CP

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6JKT \| pdb_00006jkt	Download File View File

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with N-(PHOSPHONACETYL)-L-ASPARTIC ACID (PALA).

Matoba, K., Shiba, T., Nara, T., Aoki, T., Nagasaki, S., Hayamizu, R., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Balogun, E.O., Inaoka, D.K., Kita, K., Harada, S.

To be published

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Trypanosoma cruzi
Macromolecule	Aspartate carbamoyltransferase (protein)
Unique Ligands	GOL, PAL

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6JL4 \| pdb_00006jl4	Download File View File

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl aspartate (CA) and phosphate (Pi)

Matoba, K., Shiba, T., Nara, T., Aoki, T., Nagasaki, S., Hayamizu, R., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Balogun, E.O., Inaoka, D.K., Kita, K., Harada, S.

To be published

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Trypanosoma cruzi
Macromolecule	Aspartate carbamoyltransferase (protein)
Unique Ligands	ASP, CP, NCD, PO4

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6JL5 \| pdb_00006jl5	Download File View File

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with aspartate (Asp) and phosphate (Pi).

Matoba, K., Shiba, T., Nara, T., Aoki, T., Nagasaki, S., Hayamizu, R., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Balogun, E.O., Inaoka, D.K., Kita, K., Harada, S.

To be published

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Trypanosoma cruzi
Macromolecule	Aspartate carbamoyltransferase (protein)
Unique Ligands	ASP, GOL, PO4

1 to 25 of 37 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

2ZJ2 | pdb_00002zj2

2ZJ5 | pdb_00002zj5

2ZJ8 | pdb_00002zj8

2ZJA | pdb_00002zja

3AGR | pdb_00003agr

3VI1 | pdb_00003vi1

3VKF | pdb_00003vkf

3VX6 | pdb_00003vx6

3VX7 | pdb_00003vx7

3VX8 | pdb_00003vx8

5GJE | pdb_00005gje

5JGE | pdb_00005jge

5JGF | pdb_00005jgf

5JH9 | pdb_00005jh9

5JHC | pdb_00005jhc

6AHY | pdb_00006ahy

6JI1 | pdb_00006ji1

6JKC | pdb_00006jkc

6JKD | pdb_00006jkd

6JKQ | pdb_00006jkq

6JKR | pdb_00006jkr

6JKS | pdb_00006jks

6JKT | pdb_00006jkt

6JL4 | pdb_00006jl4

6JL5 | pdb_00006jl5