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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ito, T."

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Search Summary

This query matches 161 Structures.

Refinements

Structure Determination Methodology

experimental (161)

Scientific Name of Source Organism

	Homo sapiens (61)
	synthetic construct (20)
	Mus musculus (9)
	Pyrococcus horikoshii (8)
	Bifidobacterium longum subsp. longum JCM 1217 (7)
	Bifidobacterium bifidum JCM 1254 (6)
	Haemophilus influenzae Rd KW20 (6)
	Methanocaldococcus jannaschii (6)
	Microbacterium saccharophilum (6)
	Saccharomyces cerevisiae (6)

More...

Taxonomy

	Eukaryota (87)
	Bacteria (43)
	Archaea (22)
	other sequences (20)
	Riboviria (6)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (118)
	ELECTRON MICROSCOPY (28)
	SOLUTION NMR (15)

Polymer Entity Type

	Protein (154)
	RNA (29)
	DNA (23)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (37)
	2.0 - 2.5 (49)
	2.5 - 3.0 (22)
	3.0 - 3.5 (18)
	3.5 - 4.0 (7)
	4.0 - 4.5 (5)
	> 4.5 (3)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (8)
	2005 - 2009 (20)
	2010 - 2014 (32)
	2015 - 2019 (47)
	2020 - 2024 (43)
	2025 - 2029 (9)

Enzyme Classification Name

	Hydrolases (39)
	Transferases (33)
	Lyases (6)
	Ligases (3)
	Isomerases (2)

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (100)
	Cyclic (56)
	Dihedral (1)

SCOP Classification

	Artifacts (20)
	All beta proteins (10)
	Alpha and beta proteins (a+b) (14)
	Alpha and beta proteins (a/b) (9)
	All alpha proteins (5)
	Multi-domain proteins (alpha and beta) (1)
	Small proteins (1)

AllSelected

1 to 25 of 161 Structures

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1GD5 \| pdb_00001gd5	Download File View File

SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOX NADPH OXIDASE

Hiroaki, H., Ago, T., Ito, T., Sumimoto, H., Kohda, D.

(2001) Nat Struct Biol 8: 526-530

Released	2001-06-13
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	NEUTROPHIL CYTOSOL FACTOR 1 (protein)

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1H6H \| pdb_00001h6h	Download File View File

Structure of the PX domain from p40phox bound to phosphatidylinositol 3-phosphate

Karathanassis, D., Bravo, J., Pacold, M., Perisic, O., Williams, R.L.

(2001) Mol Cell 8: 829

Released	2001-11-01
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	NEUTROPHIL CYTOSOL FACTOR 4 (protein)
Unique Ligands	GOL, PIB

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1IP9 \| pdb_00001ip9	Download File View File

SOLUTION STRUCTURE OF THE PB1 DOMAIN OF BEM1P

Terasawa, H., Noda, Y., Ito, T., Hatanaka, H., Ichikawa, S., Ogura, K., Sumimoto, H., Inagaki, F.

(2001) EMBO J 20: 3947-3956

Released	2001-08-15
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	BEM1 PROTEIN (protein)

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1IPG \| pdb_00001ipg	Download File View File

SOLUTION STRUCTURE OF THE PB1 DOMAIN OF BEM1P

Terasawa, H., Noda, Y., Ito, T., Hatanaka, H., Ichikawa, S., Ogura, K., Sumimoto, H., Inagaki, F.

(2001) EMBO J 20: 3947-3956

Released	2001-08-15
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	BEM1 PROTEIN (protein)

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1K2G \| pdb_00001k2g	Download File View File

Structural basis for the 3'-terminal guanosine recognition by the group I intron

Kitamura, Y., Muto, Y., Watanabe, S., Kim, I., Ito, T., Nishiya, Y., Sakamoto, K., Ohtsuki, T., Kawai, G., Watanabe, K., Hosono, K., Takaku, H., Katoh, E., Yamazaki, T., Inoue, T., Yokoyama, S.

(2002) RNA 8: 440-451

Released	2002-05-08
Method	SOLUTION NMR
Macromolecule	5'-R(CPAPGPAPCPUPUPCPGPGPUPCPGPCPAPGPAPGPAPUPGPG)-3' (nucleic acid)

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1NUI \| pdb_00001nui	Download File View File

Crystal Structure of the primase fragment of Bacteriophage T7 primase-helicase protein

Kato, M., Ito, T., Wagner, G., Richardson, C.C., Ellenberger, T.

(2003) Mol Cell 11: 1349-1360

Released	2003-05-27
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein)
Unique Ligands	MG, ZN

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1Q1O \| pdb_00001q1o	Download File View File

Solution Structure of the PB1 Domain of Cdc24p (Long Form)

Yoshinaga, S., Kohjima, M., Ogura, K., Yokochi, M., Takeya, R., Ito, T., Sumimoto, H., Inagaki, F.

(2003) EMBO J 22: 4888-4897

Released	2003-10-14
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 24 (protein)

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1Q8K \| pdb_00001q8k	Download File View File

Solution structure of alpha subunit of human eIF2

Ito, T., Marintchev, A., Wagner, G.

(2004) Structure 12: 1693-1704

Released	2004-09-07
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Eukaryotic translation initiation factor 2 subunit 1 (protein)

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1TZ1 \| pdb_00001tz1	Download File View File

Solution structure of the PB1 domain of CDC24P (short form)

Yoshinaga, S., Terasawa, H., Ogura, K., Noda, Y., Ito, T., Sumimoto, H., Inagaki, F.

To be published

Released	2005-09-06
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 24 (protein)

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1U2F \| pdb_00001u2f	Download File View File

SOLUTION STRUCTURE OF THE FIRST RNA-BINDING DOMAIN OF HU2AF65

Ito, T., Muto, Y., Green, M.R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1999) EMBO J 18: 4523-4534

Released	1999-08-20
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN (SPLICING FACTOR U2AF 65 KD SUBUNIT) (protein)

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2D5L \| pdb_00002d5l	Download File View File

Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis

Nakajima, Y., Ito, K., Xu, Y., Yamada, N., Onohara, Y., Yoshimoto, T.

(2006) J Mol Biology 362: 228-240

Released	2006-09-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Porphyromonas gingivalis W83
Macromolecule	dipeptidyl aminopeptidase IV, putative (protein)
Unique Ligands	SO4

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2DCM \| pdb_00002dcm	Download File View File

The Crystal Structure of S603A Mutated Prolyl Tripeptidyl Aminopeptidase Complexed with Substrate

Nakajima, Y., Ito, K., Xu, Y., Yamada, N., Onohara, Y., Yoshimoto, T.

(2006) J Mol Biology 362: 228-240

Released	2006-09-19
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Porphyromonas gingivalis W83
Macromolecule	dipeptidyl aminopeptidase IV, putative (protein)
Unique Ligands	GA0

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2DP7 \| pdb_00002dp7	Download File View File

Crystal Structure of D(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine

Juan, E.C.M., Kondo, J., Kurihara, T., Ito, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2007) Nucleic Acids Res 35: 1969-1977

Released	2007-04-17
Method	X-RAY DIFFRACTION 1.55 Å
Macromolecule	DNA (5'-D(DCPDGPDCPDGPDAPDAPDTPDUPDCPDGPDCPDG)-3') (nucleic acid)
Unique Ligands	CMY, K, MG

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2DPB \| pdb_00002dpb	Download File View File

Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine

Juan, E.C.M., Kondo, J., Kurihara, T., Ito, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2007) Nucleic Acids Res 35: 1969-1977

Released	2007-04-17
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	DNA (5'-D(DCPDGPDCPDGPDAPDAPDTPDUPDCPDGPDCPDG)-3') (nucleic acid)
Unique Ligands	CMY, K

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2DPC \| pdb_00002dpc	Download File View File

Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine

Juan, E.C.M., Kondo, J., Kurihara, T., Ito, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2007) Nucleic Acids Res 35: 1969-1977

Released	2007-04-17
Method	X-RAY DIFFRACTION 1.55 Å
Macromolecule	DNA (5'-D(DCPDGPDCPDGPDAPDAPDTP(OMU)PDCPDGPDCPDG)-3') (nucleic acid)
Unique Ligands	CMY, CO, MG

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2DQ6 \| pdb_00002dq6	Download File View File

Crystal Structure of Aminopeptidase N from Escherichia coli

Nakajima, Y., Onohara, Y., Ito, K., Yoshimoto, T.

(2006) J Biological Chem 281: 33664-33676

Released	2006-08-01
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli
Macromolecule	Aminopeptidase N (protein)
Unique Ligands	SO4, ZN

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2DQM \| pdb_00002dqm	Download File View File

Crystal Structure of Aminopeptidase N complexed with bestatin

Onohara, Y., Nakajima, Y., Ito, K., Yoshimoto, T.

(2006) J Biological Chem 281: 33664-33676

Released	2006-08-01
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Escherichia coli
Macromolecule	Aminopeptidase N (protein)
Unique Ligands	BES, SO4, ZN

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2DQO \| pdb_00002dqo	Download File View File

Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine

Juan, E.C.M., Kondo, J., Ito, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2007) Nucleic Acids Res 35: 1969-1977

Released	2007-04-17
Method	X-RAY DIFFRACTION 2.3 Å
Macromolecule	DNA (5'-D(DCP(OMU)PDCPDTP(OMU)PDCPDTPDTPDC)-3') (nucleic acid) RNA (5'-R(GPAPAPGPAPAPGPAPG)-3') (nucleic acid)
Unique Ligands	BA, CMY, NA

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2DQP \| pdb_00002dqp	Download File View File

Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines

Juan, E.C.M., Kondo, J., Ito, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2007) Nucleic Acids Res 35: 1969-1977

Released	2007-04-17
Method	X-RAY DIFFRACTION 2.1 Å
Macromolecule	DNA (5'-D(DCP(OMU)PDCPDTP(OMU)PDCPDTPDTPDC)-3') (nucleic acid) RNA (5'-R(GPAPAPGPAPAPGPAPG)-3') (nucleic acid)
Unique Ligands	CMY

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2DQQ \| pdb_00002dqq	Download File View File

Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine

Juan, E.C.M., Kondo, J., Ito, T., Ueno, Y., Matsuda, A., Takenaka, A.

(2007) Nucleic Acids Res 35: 1969-1977

Released	2007-04-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(DCP(OMU)PDCPDTP(OMU)PDCPDTPDTPDC)-3') (nucleic acid) RNA (5'-R(GPAPAPGPAPAPGPAPG)-3') (nucleic acid)
Unique Ligands	CMY

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2KFJ \| pdb_00002kfj	Download File View File

Solution structure of the loop deletion mutant of PB1 domain of Cdc24p

Ogura, K., Tandai, T., Yoshinaga, S., Kobashigawa, Y., Kumeta, H., Inagaki, F.

(2009) J Biochem 146: 317-325

Released	2009-10-06
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 24 (protein)

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2KFK \| pdb_00002kfk	Download File View File

Solution structure of Bem1p PB1 domain complexed with Cdc24p PB1 domain

Kobashigawa, Y., Yoshinaga, S., Tandai, T., Ogura, K., Inagaki, F.

(2009) J Biochem 146: 317-325

Released	2009-10-06
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Bud emergence protein 1 (protein) Cell division control protein 24 (protein)

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2MGZ \| pdb_00002mgz	Download File View File

Solution structure of RBFOX family ASD-1 RRM and SUP-12 RRM in ternary complex with RNA

Takahashi, M., Kuwasako, K., Unzai, S., Tsuda, K., Yoshikawa, S., He, F., Kobayashi, N., Guntert, P., Shirouzu, M., Ito, T., Tanaka, A., Yokoyama, S., Hagiwara, M., Kuroyanagi, H., Muto, Y.

(2014) Nat Struct Mol Biol 21: 778-786

Released	2014-08-13
Method	SOLUTION NMR
Organisms	Caenorhabditis elegans
Macromolecule	Protein ASD-1, isoform a (protein) Protein SUP-12, isoform a (protein) RNA (5'-R(UPGPCPAPUPGPGPUPGPUPGPC)-3') (nucleic acid)

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2RQR \| pdb_00002rqr	Download File View File

The solution structure of human DOCK2 SH3 domain - ELMO1 peptide chimera complex

Yokoyama, S., Tochio, N., Koshiba, S., Kigawa, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2012) Proc Natl Acad Sci U S A 109: 3305-3310

Released	2010-10-27
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Engulfment and cell motility protein 1,Dedicator of cytokinesis protein 2 (protein)

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2RU3 \| pdb_00002ru3	Download File View File

Solution structure of c.elegans SUP-12 RRM in complex with RNA

Takahashi, M., Kuwasako, K., Unzai, S., Tsuda, K., Yoshikawa, S., He, F., Kobayashi, N., Guntert, P., Shirouzu, M., Ito, T., Tanaka, A., Yokoyama, S., Hagiwara, M., Kuroyanagi, H., Muto, Y.

(2014) Nat Struct Mol Biol 21: 778-786

Released	2014-08-13
Method	SOLUTION NMR
Organisms	Caenorhabditis elegans
Macromolecule	Protein SUP-12, isoform a (protein) RNA (5'-R(GPUPGPUPGPC)-3') (nucleic acid)

1 to 25 of 161 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

1GD5 | pdb_00001gd5

1H6H | pdb_00001h6h

1IP9 | pdb_00001ip9

1IPG | pdb_00001ipg

1K2G | pdb_00001k2g

1NUI | pdb_00001nui

1Q1O | pdb_00001q1o

1Q8K | pdb_00001q8k

1TZ1 | pdb_00001tz1

1U2F | pdb_00001u2f

2D5L | pdb_00002d5l

2DCM | pdb_00002dcm

2DP7 | pdb_00002dp7

2DPB | pdb_00002dpb

2DPC | pdb_00002dpc

2DQ6 | pdb_00002dq6

2DQM | pdb_00002dqm

2DQO | pdb_00002dqo

2DQP | pdb_00002dqp

2DQQ | pdb_00002dqq

2KFJ | pdb_00002kfj

2KFK | pdb_00002kfk

2MGZ | pdb_00002mgz

2RQR | pdb_00002rqr

2RU3 | pdb_00002ru3