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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Natarajan, C."

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Homo sapiens (12)
	Saccharomyces cerevisiae (4)
	Listeria innocua (3)
	Listeria innocua Clip11262 (2)
	Aeropyrum pernix (1)
	Aeropyrum pernix K1 (1)
	Saccharomyces cerevisiae S288C (1)
	Schizosaccharomyces pombe (1)

Taxonomy

	Eukaryota (18)
	Bacteria (5)
	Archaea (1)

Experimental Method

	SOLUTION NMR (18)
	X-RAY DIFFRACTION (6)

Polymer Entity Type

Protein (24)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (1)
	2.5 - 3.0 (2)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (6)
	2010 - 2014 (2)
	2015 - 2019 (8)
	2020 - 2024 (5)

Enzyme Classification Name

	Oxidoreductases (5)
	Hydrolases (3)
	Transferases (2)
	Lyases (1)

Symmetry Type

	Asymmetric (18)
	Tetrahedral (5)
	Cyclic (1)

SCOP Classification

	All alpha proteins (7)
	All beta proteins (6)
	Artifacts (1)
	Small proteins (1)

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1 to 24 of 24 Structures

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1D8J \| pdb_00001d8j	Download File View File

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

Okuda, M., Watanabe, Y., Okamura, H., Hanaoka, F., Ohkuma, Y., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) EMBO J 19: 1346-1356

Released	2000-04-26
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	GENERAL TRANSCRIPTION FACTOR TFIIE-BETA (protein)

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1D8K \| pdb_00001d8k	Download File View File

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

Okuda, M., Watanabe, Y., Okamura, H., Hanaoka, F., Ohkuma, Y., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) EMBO J 19: 1346-1356

Released	2000-04-26
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	GENERAL TRANSCRIPTION FACTOR TFIIE-BETA (protein)

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1VD4 \| pdb_00001vd4	Download File View File

Solution structure of the zinc finger domain of TFIIE alpha

Okuda, M., Tanaka, A., Arai, Y., Satoh, M., Okamura, H., Nagadoi, A., Hanaoka, F., Ohkuma, Y., Nishimura, Y.

(2004) J Biological Chem 279: 51395-51403

Released	2004-10-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription initiation factor IIE, alpha subunit (protein)
Unique Ligands	ZN

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2DY7 \| pdb_00002dy7	Download File View File

Solution structure of the first chromodomain of yeast Chd1

Okuda, M., Nishimura, Y.

(2007) J Mol Biology 365: 1047-1062

Released	2006-11-28
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Chromo domain protein 1 (protein)

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2DY8 \| pdb_00002dy8	Download File View File

Solution structure of the second chromodomain of yeast Chd1

Okuda, M., Nishimura, Y.

(2007) J Mol Biology 365: 1047-1062

Released	2006-11-28
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Chromo domain protein 1 (protein)

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2RNQ \| pdb_00002rnq	Download File View File

Solution structure of the C-terminal acidic domain of TFIIE alpha

Okuda, M., Nishimura, Y.

(2008) EMBO J 27: 1161-1171

Released	2008-04-01
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription initiation factor IIE subunit alpha (protein)

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2RNR \| pdb_00002rnr	Download File View File

Solution structure of the complex between TFIIE alpha C-terminal acidic domain and TFIIH p62 PH domain

Okuda, M., Nishimura, Y.

(2008) EMBO J 27: 1161-1171

Released	2008-04-01
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TFIIH basal transcription factor complex p62 subunit (protein) Transcription initiation factor IIE subunit alpha (protein)

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2RNZ \| pdb_00002rnz	Download File View File

Solution structure of the presumed chromodomain of the yeast histone acetyltransferase, Esa1

Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., Nishimura, Y.

(2008) J Mol Biology 378: 987-1001

Released	2008-04-29
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Histone acetyltransferase ESA1 (protein)

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2RO0 \| pdb_00002ro0	Download File View File

Solution structure of the knotted tudor domain of the yeast histone acetyltransferase, Esa1

Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., Nishimura, Y.

(2008) J Mol Biology 378: 987-1001

Released	2008-04-29
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Histone acetyltransferase ESA1 (protein)

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2RUK \| pdb_00002ruk	Download File View File

Solution structure of the complex between p53 transactivation domain 2 and TFIIH p62 PH domain

Okuda, M., Nishimura, Y.

(2014) J Am Chem Soc 136: 14143-14152

Released	2014-10-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Cellular tumor antigen p53 (protein) General transcription factor IIH subunit 1 (protein)

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2RVB \| pdb_00002rvb	Download File View File

Solution structure of the complex between XPC acidic domain and TFIIH p62 PH domain

Okuda, M., Nishimura, Y.

(2015) Structure 23: 1827-1837

Released	2015-09-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	DNA repair protein complementing XP-C cells (protein) General transcription factor IIH subunit 1 (protein)

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3AJV \| pdb_00003ajv	Download File View File

Splicing endonuclease from Aeropyrum pernix

Yoshinari, S., Watanabe, Y., Okuda, M., Shiba, T., Inaoka, K.D., Kurisu, G.

(2011) J Mol Biology 405: 92-104

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Aeropyrum pernix Aeropyrum pernix K1
Macromolecule	Putative uncharacterized protein (protein) tRNA-splicing endonuclease (protein)
Unique Ligands	CL, GOL

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5GOW \| pdb_00005gow	Download File View File

Solution structure of the complex between DP1 acidic region and TFIIH p62 PH domain

Okuda, M., Nishimura, Y.

(2016) J Mol Biology 428: 4993-5006

Released	2016-12-07
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	DP1 (protein) General transcription factor IIH subunit 1 (protein)

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5XV8 \| pdb_00005xv8	Download File View File

Solution structure of the complex between UVSSA acidic region and TFIIH p62 PH domain

Okuda, M., Nishimura, Y.

(2017) Nucleic Acids Res 45: 13043-13055

Released	2017-11-08
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	General transcription factor IIH subunit 1 (protein) UV-stimulated scaffold protein A (protein)

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6HUI \| pdb_00006hui	Download File View File

The structure of Dps from Listeria innocua soaked with zinc

Zeth, K., Okuda, M.

(2019) Inorg Chem 58: 11351-11363

Released	2019-09-04
Method	X-RAY DIFFRACTION 2.995 Å
Organisms	Listeria innocua
Macromolecule	DNA protection during starvation protein (protein)
Unique Ligands	ZN

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6HV1 \| pdb_00006hv1	Download File View File

The apo structure of Dps from Listeria innocua before soaking experiments with Zn, Co and La

Zeth, K., Okuda, M.

(2019) Inorg Chem 58: 11351-11363

Released	2018-11-14
Method	X-RAY DIFFRACTION 2.547 Å
Organisms	Listeria innocua
Macromolecule	DNA protection during starvation protein (protein)

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6HVQ \| pdb_00006hvq	Download File View File

The structure of Dps from Listeria innocua soaked before soaking experiments with Zn, Co and La

Zeth, K., Okuda, M.

(2019) Inorg Chem 58: 11351-11363

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Listeria innocua Clip11262
Macromolecule	DNA protection during starvation protein (protein)
Unique Ligands	LA

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6HX2 \| pdb_00006hx2	Download File View File

The structure of Dps from Listeria innocua soaked with Cobalt

Zeth, K., Okuda, M.

(2019) Inorg Chem 58: 11351-11363

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.597 Å
Organisms	Listeria innocua Clip11262
Macromolecule	DNA protection during starvation protein (protein)
Unique Ligands	CO

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6K5W \| pdb_00006k5w	Download File View File

Solution structure of the chromodomain of yeast Eaf3

Okuda, M., Nishimura, Y.

(2020) Biosci Rep 40:

Released	2020-02-26
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Chromatin modification-related protein EAF3 (protein)

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6SEV \| pdb_00006sev	Download File View File

Structure of Dps from Listeria innocua soaked with 10 mM zinc for 120 minutes

Zeth, K., Okuda, M.

(2019) Inorg Chem 58: 11351-11363

Released	2019-09-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Listeria innocua
Macromolecule	DNA starvation/stationary phase protection protein (protein)
Unique Ligands	ZN

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7BUL \| pdb_00007bul	Download File View File

Solution structure of the tandem PH and BSD1 domains of TFIIH p62

Okuda, M., Nishimura, Y.

(2021) Nucleic Acids Res 49: 2916-2930

Released	2020-12-30
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	General transcription factor IIH subunit 1 (protein)

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7DTH \| pdb_00007dth	Download File View File

Solution structure of RPB6, common subunit of RNA polymerases I, II, and III

Okuda, M., Nishimura, Y.

(2022) Nucleic Acids Res 50: 1-16

Released	2022-01-19
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	DNA-directed RNA polymerases I, II, and III subunit RPABC2 (protein)

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7DTI \| pdb_00007dti	Download File View File

Solution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain

Okuda, M., Nishimura, Y.

(2022) Nucleic Acids Res 50: 1-16

Released	2022-08-10
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	DNA-directed RNA polymerases I, II, and III subunit RPABC2 (protein) General transcription factor IIH subunit 1 (protein)

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8I53 \| pdb_00008i53	Download File View File

Solution structure of the PH domain from the Tfb1 subunit of fission yeast TFIIH

Okuda, M., Nishimura, Y.

(2023) Biosci Rep 43:

Released	2023-11-01
Method	SOLUTION NMR
Organisms	Schizosaccharomyces pombe
Macromolecule	General transcription and DNA repair factor IIH subunit tfb1 (protein)

1 to 24 of 24 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

Symmetry Type

SCOP Classification

1D8J | pdb_00001d8j

1D8K | pdb_00001d8k

1VD4 | pdb_00001vd4

2DY7 | pdb_00002dy7

2DY8 | pdb_00002dy8

2RNQ | pdb_00002rnq

2RNR | pdb_00002rnr

2RNZ | pdb_00002rnz

2RO0 | pdb_00002ro0

2RUK | pdb_00002ruk

2RVB | pdb_00002rvb

3AJV | pdb_00003ajv

5GOW | pdb_00005gow

5XV8 | pdb_00005xv8

6HUI | pdb_00006hui

6HV1 | pdb_00006hv1

6HVQ | pdb_00006hvq

6HX2 | pdb_00006hx2

6K5W | pdb_00006k5w

6SEV | pdb_00006sev

7BUL | pdb_00007bul

7DTH | pdb_00007dth

7DTI | pdb_00007dti

8I53 | pdb_00008i53