RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Citation Author = "Nishimura, Y."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 73 Structures.

Refinements

Structure Determination Methodology

experimental (73)

Scientific Name of Source Organism

	Homo sapiens (36)
	Mus musculus (19)
	synthetic construct (7)
	Escherichia coli (4)
	Saccharomyces cerevisiae (4)
	Human immunodeficiency virus 1 (3)
	Schizosaccharomyces pombe (2)
	Schizosaccharomyces pombe 972h- (2)
	Anthopleura elegantissima (1)
	Calothrix sp. NIES-2098 (1)

More...

Taxonomy

	Eukaryota (63)
	Bacteria (8)
	other sequences (7)
	Riboviria (3)
	Eukaryota (eukaryotes) (2)
	Archaea (1)

Experimental Method

	SOLUTION NMR (52)
	X-RAY DIFFRACTION (19)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

	Protein (73)
	DNA (8)

Refinement Resolution (Å)

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

Release Date

	1995 - 1999 (15)
	2000 - 2004 (8)
	2005 - 2009 (15)
	2010 - 2014 (9)
	2015 - 2019 (11)
	2020 - 2024 (15)

Enzyme Classification Name

	Hydrolases (10)
	Transferases (2)

Membrane Protein Annotation

	PDBTM (2)
	MemProtMD (1)
	OPM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (65)
	Cyclic (8)

SCOP Classification

	All alpha proteins (26)
	All beta proteins (12)
	Artifacts (5)
	Alpha and beta proteins (a+b) (3)
	Membrane and cell surface proteins and peptides (2)
	Small proteins (2)

AllSelected

1 to 25 of 73 Structures

Page 1 of 3

Sort by

Explore in 3D

1BA5 \| pdb_00001ba5	Download File View File

DNA-BINDING DOMAIN OF HUMAN TELOMERIC PROTEIN, HTRF1, NMR, 18 STRUCTURES

Nishikawa, T., Nagadoi, A., Yoshimura, S., Aimoto, S., Nishimura, Y.

(1998) Structure 6: 1057-1065

Released	1999-04-27
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HTRF1 (protein)

Explore in 3D

1BHI \| pdb_00001bhi	Download File View File

STRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STRUCTURES

Nagadoi, A., Nakazawa, K., Uda, H., Maekawa, T., Ishii, S., Nishimura, Y.

(1999) J Mol Biology 287: 593-607

Released	1999-06-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	CRE-BP1 (protein)

Explore in 3D

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)

Explore in 3D

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)

Explore in 3D

1FEX \| pdb_00001fex	Download File View File

SOLUTION STRUCTURE OF MYB-DOMAIN OF HUMAN RAP1

Hanaoka, S., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) J Mol Biology 312: 167-175

Released	2001-09-19
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TRF2-INTERACTING TELOMERIC RAP1 PROTEIN (protein)

Explore in 3D

1IDY \| pdb_00001idy	Download File View File

STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE

Furukawa, K., Oda, M., Nakamura, H.

(1996) Proc Natl Acad Sci U S A 93: 13583-13588

Released	1996-12-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 (protein)

Explore in 3D

1IDZ \| pdb_00001idz	Download File View File

STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, 20 STRUCTURES

Furukawa, K., Oda, M., Nakamura, H.

(1996) Proc Natl Acad Sci U S A 93: 13583-13588

Released	1996-12-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 (protein)

Explore in 3D

1ITY \| pdb_00001ity	Download File View File

Solution structure of the DNA binding domain of human TRF1

Nishikawa, T., Okamura, H., Nagadoi, A., Konig, P., Rhodes, D., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Structure 9: 1237-1251

Released	2002-03-06
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TRF1 (protein)

Explore in 3D

1IV6 \| pdb_00001iv6	Download File View File

Solution Structure of the DNA Complex of Human TRF1

Nishikawa, T., Okamura, H., Nagadoi, A., Konig, P., Rhodes, D., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Structure 9: 1237-1251

Released	2002-04-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TELOMERIC REPEAT BINDING FACTOR 1 (protein) 5'-D(CPCPCPTPAPAPCPCPCPTPAPAPC)-3' (nucleic acid) 5'-D(GPTPTPAPGPGPGPTPTPAPGPGPG)-3' (nucleic acid)

Explore in 3D

1J05 \| pdb_00001j05	Download File View File

The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment

Kondo, H., Nishimura, Y., Shiroishi, M., Asano, R., Noro, N., Tsumoto, K., Kumagai, I.

To be published

Released	2003-12-16
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mus musculus
Macromolecule	anti-CEA mAb T84.66, heavy chain (protein) anti-CEA mAb T84.66, light chain (protein)
Unique Ligands	GOL, PO4

Explore in 3D

1MBE \| pdb_00001mbe	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

Explore in 3D

1MBF \| pdb_00001mbf	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

Explore in 3D

1MBG \| pdb_00001mbg	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 2

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

Explore in 3D

1MBH \| pdb_00001mbh	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 2

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-09-15
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	C-MYB (protein)

Explore in 3D

1MBJ \| pdb_00001mbj	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

Explore in 3D

1MBK \| pdb_00001mbk	Download File View File

MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3

Ogata, K., Morikawa, S., Nakamura, H., Hojo, H., Yoshimura, S., Zhang, R., Aimoto, S., Ametani, Y., Hirata, Z., Sarai, A., Ishii, S., Nishimura, Y.

(1995) Nat Struct Biol 2: 309-320

Released	1995-07-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MYB PROTO-ONCOGENE PROTEIN (protein)

Explore in 3D

1MSE \| pdb_00001mse	Download File View File

SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES

Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

(1994) Cell 79: 639-648

Released	1995-03-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	C-Myb DNA-Binding Domain (protein) DNA (5'-D(APTPGPTPGPTPGPTPCPAPGPTPTPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPAPAPCPTPGPAPCPAPCPAPCPAPT)-3') (nucleic acid)

Explore in 3D

1MSF \| pdb_00001msf	Download File View File

SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES

Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

(1994) Cell 79: 639-648

Released	1995-03-31
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	C-Myb DNA-Binding Domain (protein) DNA (5'-D(APTPGPTPGPTPGPTPCPAPGPTPTPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPAPAPCPTPGPAPCPAPCPAPCPAPT)-3') (nucleic acid)

Explore in 3D

1ODD \| pdb_00001odd	Download File View File

OMPR C-TERMINAL DOMAIN (OMPR-C) FROM ESCHERICHIA COLI

Kondou, H., Nakagawa, A., Tanaka, I.

(1997) Nat Struct Biol 4: 28-31

Released	1997-05-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli K-12
Macromolecule	TRANSCRIPTIONAL REGULATORY PROTEIN OMPR (protein)

Explore in 3D

1PRU \| pdb_00001pru	Download File View File

PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING

Nagadoi, A., Morikawa, S., Nakamura, H., Enari, M., Kobayashi, K., Yamamoto, H., Sampei, G., Mizobuchi, K., Schumacher, M.A., Brennan, R.G., Nishimura, Y.

(1995) Structure 3: 1217-1224

Released	1996-03-08
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PURINE REPRESSOR (protein)

Explore in 3D

1PRV \| pdb_00001prv	Download File View File

PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING

Nagadoi, A., Morikawa, S., Nakamura, H., Enari, M., Kobayashi, K., Yamamoto, H., Sampei, G., Mizobuchi, K., Schumacher, M.A., Brennan, R.G., Nishimura, Y.

(1995) Structure 3: 1217-1224

Released	1996-03-08
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PURINE REPRESSOR (protein)

Explore in 3D

1QQI \| pdb_00001qqi	Download File View File

SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI

Okamura, H., Hanaoka, S., Nagadoi, A., Makino, K., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) J Mol Biology 295: 1225-1236

Released	2000-06-07
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB (protein)

Explore in 3D

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

Explore in 3D

1VF9 \| pdb_00001vf9	Download File View File

Solution Structure Of Human Trf2

Nishimura, Y., Hanaoka, S.

(2005) Protein Sci 14: 119-130

Released	2005-05-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Telomeric repeat binding factor 2 (protein)

Explore in 3D

1VFC \| pdb_00001vfc	Download File View File

Solution Structure Of The DNA Complex Of Human Trf2

Nishimura, Y., Hanaoka, S.

(2005) Protein Sci 14: 119-130

Released	2005-05-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Telomeric repeat binding factor 2 (protein) Short C-rich starnd (nucleic acid) Short G-rich strand (nucleic acid)

1 to 25 of 73 Structures

Page 1 of 3

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

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

1BA5 | pdb_00001ba5

1BHI | pdb_00001bhi

1D8J | pdb_00001d8j

1D8K | pdb_00001d8k

1FEX | pdb_00001fex

1IDY | pdb_00001idy

1IDZ | pdb_00001idz

1ITY | pdb_00001ity

1IV6 | pdb_00001iv6

1J05 | pdb_00001j05

1MBE | pdb_00001mbe

1MBF | pdb_00001mbf

1MBG | pdb_00001mbg

1MBH | pdb_00001mbh

1MBJ | pdb_00001mbj

1MBK | pdb_00001mbk

1MSE | pdb_00001mse

1MSF | pdb_00001msf

1ODD | pdb_00001odd

1PRU | pdb_00001pru

1PRV | pdb_00001prv

1QQI | pdb_00001qqi

1VD4 | pdb_00001vd4

1VF9 | pdb_00001vf9

1VFC | pdb_00001vfc