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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Ishitani, R."

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Search Summary

This query matches 199 Structures.

Refinements

Structure Determination Methodology

experimental (199)

Scientific Name of Source Organism

	Mus musculus (24)
	Homo sapiens (19)
	Thermus thermophilus HB8 (14)
	synthetic construct (10)
	Chlamydomonas reinhardtii (8)
	Archaeoglobus fulgidus (7)
	Geobacillus kaustophilus (7)
	Methanocaldococcus jannaschii (7)
	Pyrococcus horikoshii (7)
	Eucalyptus grandis (6)

More...

Taxonomy

	Bacteria (88)
	Eukaryota (78)
	Archaea (34)
	other sequences (10)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (195)
	ELECTRON MICROSCOPY (4)

Polymer Entity Type

	Protein (199)
	RNA (35)
	DNA (21)
	NA-hybrid (1)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (47)
	2.0 - 2.5 (65)
	2.5 - 3.0 (56)
	3.0 - 3.5 (19)
	3.5 - 4.0 (7)
	4.0 - 4.5 (3)

Release Date

	2000 - 2004 (14)
	2005 - 2009 (37)
	2010 - 2014 (62)
	2015 - 2019 (78)
	2020 - 2024 (8)

Enzyme Classification Name

	Transferases (52)
	Hydrolases (46)
	Ligases (11)
	Lyases (4)
	Oxidoreductases (2)

Membrane Protein Annotation

	PDBTM (55)
	mpstruc (50)
	MemProtMD (48)
	OPM (36)

Symmetry Type

	Asymmetric (147)
	Cyclic (56)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (23)
	Alpha and beta proteins (a/b) (21)
	All beta proteins (9)
	All alpha proteins (13)
	Membrane and cell surface proteins and peptides (11)
	Artifacts (7)
	Small proteins (1)
	Multi-domain proteins (alpha and beta) (2)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 199 Structures

Page 1 of 8

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1IPA \| pdb_00001ipa	Download File View File

CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE

Nureki, O., Shirouzu, M., Hashimoto, K., Ishitani, R., Terada, T., Tamakoshi, M., Oshima, T., Chijimatsu, M., Takio, K., Vassylyev, D.G., Shibata, T., Inoue, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Acta Crystallogr D Biol Crystallogr 58: 1129-1137

Released	2002-07-10
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	RNA 2'-O-RIBOSE METHYLTRANSFERASE (protein)

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1IQ8 \| pdb_00001iq8	Download File View File

Crystal Structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii

Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 318: 665-677

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus horikoshii
Macromolecule	ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE (protein)
Unique Ligands	MG, ZN

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1IRX \| pdb_00001irx	Download File View File

Crystal structure of class I lysyl-tRNA synthetase

Nureki, O., Terada, T., Ishitani, R., Ambrogelly, A., Ibba, M., Soll, D., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Nat Struct Biol 9: 257-262

Released	2002-04-17
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus horikoshii
Macromolecule	lysyl-tRNA synthetase (protein)
Unique Ligands	ZN

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1IT7 \| pdb_00001it7	Download File View File

Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine

Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 318: 665-677

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Archaeosine tRNA-guanine transglycosylase (protein)
Unique Ligands	GUN, MG, ZN

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1IT8 \| pdb_00001it8	Download File View File

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 318: 665-677

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus horikoshii
Macromolecule	archaeosine tRNA-guanine transglycosylase (protein)
Unique Ligands	MG, PQ0, ZN

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1IUG \| pdb_00001iug	Download File View File

The crystal structure of aspartate aminotransferase which belongs to subgroup IV from Thermus thermophilus

Katsura, Y., Shirouzu, M., Yamaguchi, H., Ishitani, R., Nureki, O., Kuramitsu, S., Hayashi, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Proteins 55: 487-492

Released	2003-11-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	putative aspartate aminotransferase (protein)
Unique Ligands	PO4

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1IVO \| pdb_00001ivo	Download File View File

Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.

Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.H., Saito, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Cell 110: 775-787

Released	2002-10-16
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Epidermal Growth Factor Receptor (protein) Epidermal growth factor (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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1J1U \| pdb_00001j1u	Download File View File

Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine

Kobayashi, T., Nureki, O., Ishitani, R., Tukalo, M., Cusack, S., Sakamoto, K., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Nat Struct Biol 10: 425-432

Released	2003-06-03
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Tyrosyl-tRNA synthetase (protein) tRNA(Tyr) (nucleic acid)
Unique Ligands	MG, TYR

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1J2B \| pdb_00001j2b	Download File View File

Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)

Ishitani, R., Nureki, O., Nameki, N., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Cell 113: 383-394

Released	2003-05-27
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Archaeosine tRNA-guanine transglycosylase (protein) tRNA(Val) (nucleic acid)
Unique Ligands	MG, ZN

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1KN0 \| pdb_00001kn0	Download File View File

Crystal Structure of the human Rad52 protein

Kagawa, W., Kurumizaka, H., Ishitani, R., Fukai, S., Nureki, O., Shibata, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Mol Cell 10: 359-371

Released	2002-09-04
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	Rad52 (protein)

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1UDZ \| pdb_00001udz	Download File View File

Isoleucyl-tRNA synthetase editing domain

Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 8396-8402

Released	2004-03-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus
Macromolecule	Isoleucyl-tRNA synthetase (protein)

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1UE0 \| pdb_00001ue0	Download File View File

Isoleucyl-tRNA synthetase editing domain complexed with L-Valine

Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 8396-8402

Released	2004-03-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	Isoleucyl-tRNA synthetase (protein)
Unique Ligands	VAL

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1UFA \| pdb_00001ufa	Download File View File

Crystal structure of TT1467 from Thermus thermophilus HB8

Idaka, M., Terada, T., Murayama, K., Yamaguchi, H., Nureki, O., Ishitani, R., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-11-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	TT1467 protein (protein)

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1VFG \| pdb_00001vfg	Download File View File

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog

Tomita, K., Fukai, S., Ishitani, R., Ueda, T., Takeuchi, N., Vassylyev, D.G., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Nature 430: 700-704

Released	2004-08-10
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Aquifex aeolicus
Macromolecule	poly A polymerase (protein) RNA (75-MER) (nucleic acid)
Unique Ligands	APC

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2DR5 \| pdb_00002dr5	Download File View File

Complex structure of CCA adding enzyme with mini-helix lacking CCA

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-10-31
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (32-MER) (nucleic acid)
Unique Ligands	SO4

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2DR7 \| pdb_00002dr7	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDC

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (33-MER) (nucleic acid)
Unique Ligands	SO4

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2DR8 \| pdb_00002dr8	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDC and CTP

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (33-MER) (nucleic acid)
Unique Ligands	CTP, MG, SO4

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2DR9 \| pdb_00002dr9	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDCC

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (34-MER) (nucleic acid)
Unique Ligands	SO4

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2DRA \| pdb_00002dra	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (34-MER) (nucleic acid)
Unique Ligands	ATP, MG, SO4

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2DRB \| pdb_00002drb	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiCCA

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (35-MER) (nucleic acid)
Unique Ligands	SO4

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2DVI \| pdb_00002dvi	Download File View File

Complex structure of CCA-adding enzyme, mini-DCC and CTP

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (34-MER) (nucleic acid)
Unique Ligands	CTP, MG, SO4

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2EQB \| pdb_00002eqb	Download File View File

Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex

Sato, Y., Fukai, S., Ishitani, R., Nureki, O.

(2007) Proc Natl Acad Sci U S A 104: 8305-8310

Released	2007-05-22
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Rab guanine nucleotide exchange factor SEC2 (protein) Ras-related protein SEC4 (protein)
Unique Ligands	PO4