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

232,418 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: Structure Author = "Kawazoe, M."

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 28 Structures.

Refinements

Structure Determination Methodology

experimental (28)

Scientific Name of Source Organism

	Thermus thermophilus HB8 (11)
	Aquifex aeolicus VF5 (4)
	Homo sapiens (3)
	Mus musculus (2)
	Schistosoma japonicum (2)
	Thermus thermophilus (2)
	synthetic construct (2)
	Aeropyrum pernix K1 (1)
	Escherichia coli O157:H7 (1)
	Pyrococcus horikoshii (1)

More...

Taxonomy

	Bacteria (19)
	Eukaryota (7)
	Archaea (2)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (24)
	ELECTRON MICROSCOPY (2)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (28)
	RNA (3)

Refinement Resolution (Å)

	1.5 - 2.0 (9)
	2.0 - 2.5 (8)
	2.5 - 3.0 (3)
	3.0 - 3.5 (4)
	> 4.5 (2)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (22)
	2010 - 2014 (3)
	2015 - 2019 (2)

Enzyme Classification Name

	Lyases (2)
	Transferases (2)

Symmetry Type

	Asymmetric (24)
	Cyclic (4)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (8)
	Alpha and beta proteins (a/b) (7)
	All alpha proteins (4)
	All beta proteins (2)
	Artifacts (3)
	Low resolution protein structures (1)
	Peptides (1)
	Small proteins (1)

AllSelected

1 to 25 of 28 Structures

Page 1 of 2

Sort by

Explore in 3D

1WF3	Download File View File

Crystal structure of GTP-binding protein TT1341 from Thermus thermophilus HB8

Kawazoe, M., Hori-Takemoto, C., Kaminishi, T., Sekine, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-25
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Thermus thermophilus HB8
Macromolecule	GTP-binding protein (protein)
Unique Ligands	GNP, GOL, MG

Explore in 3D

2CX6	Download File View File

Crystal structure of ribonuclease inhibitor Barstar

Murayama, K., Kawazoe, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-12-28
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Escherichia coli O157:H7
Macromolecule	Hypothetical protein yhcO (protein)

Explore in 3D

2CXH	Download File View File

Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1

Kawazoe, M., Takemoto, C., Hanawa-Suetsugu, K., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-12-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable brix-domain ribosomal biogenesis protein (protein)

Explore in 3D

2DOG	Download File View File

Solution structure of the N-terminal domain of RimM from Thermus thermophilus HB8

Suzuki, S., Matsumoto, E., Tatsuguchi, A., Kawazoe, M., Kaminishi, T., Takemoto, C., Shirouzu, M., Muto, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) J Bacteriol 189: 6397-6406

Released	2007-04-17
Method	SOLUTION NMR
Organisms	Thermus thermophilus HB8
Macromolecule	Probable 16S rRNA-processing protein rimM (protein)

Explore in 3D

2DYI	Download File View File

Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Probable 16S rRNA-processing protein rimM (protein)

Explore in 3D

2DYJ	Download File View File

Crystal structure of ribosome-binding factor A from Thermus thermophilus HB8

Kawazoe, M., Takemoto, C., Nakayama-Ushikoshi, R., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Mol Cell 28: 434-445

Released	2007-03-14
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribosome-binding factor A (protein)

Explore in 3D

2DYK	Download File View File

Crystal structure of N-terminal GTP-binding domain of EngA from Thermus thermophilus HB8

Kawazoe, M., Takemoto, C., Fusatomi, E., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-03-14
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Thermus thermophilus HB8
Macromolecule	GTP-binding protein (protein)
Unique Ligands	GDP

Explore in 3D

2E5L	Download File View File

A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine- Dalgarno interaction

Kaminishi, T., Wilson, D.N., Takemoto, C., Harms, J.M., Kawazoe, M., Schluenzen, F., Hanawa-Suetsugu, K., Shirouzu, M., Fucini, P., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Structure 15: 289-297

Released	2007-05-15
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Thermus thermophilus synthetic construct
Macromolecule	Unique protein chains: 20 Unique nucleic acid chains: 2
Unique Ligands	ZN

Explore in 3D

2KHE	Download File View File

Solution Structure of the Bacterial Toxin Rele from Thermus Thermophilus HB8

Suzuki, S., Kawazoe, M., Kaminishi, T., Takemoto, C., Muto, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2010-03-31
Method	SOLUTION NMR
Organisms	Thermus thermophilus HB8
Macromolecule	Toxin-like protein (protein)

Explore in 3D

2PA2	Download File View File

Crystal structure of human Ribosomal protein L10 core domain

Nishimura, M., Kaminishi, T., Takemoto, C., Kawazoe, M., Yoshida, T., Tanaka, A., Sugano, S., Shirouzu, M., Ohkubo, T., Yokoyama, S., Kobayashi, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Mol Biol 377: 421-430

Released	2008-03-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	60S ribosomal protein L10 (protein)
Unique Ligands	K

Explore in 3D

2R1C	Download File View File

Coordinates of the thermus thermophilus ribosome binding factor A (RbfA) homology model as fitted into the CRYO-EM map of a 30S-RBFA complex

Datta, P.P., Wilson, D.N., Kawazoe, M., Swami, N.K., Kaminishi, T., Sharma, M.R., Booth, T.M., Takemoto, C., Fucini, P., Yokoyama, S., Agrawal, R.K.

(2007) Mol Cell 28: 434-445

Released	2008-03-18
Method	ELECTRON MICROSCOPY 12.5 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribosome-binding factor A (protein)

Explore in 3D

2R1G	Download File View File

Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex

Datta, P.P., Wilson, D.N., Kawazoe, M., Swami, N.K., Kaminishi, T., Sharma, M.R., Booth, T.M., Takemoto, C., Fucini, P., Yokoyama, S., Agrawal, R.K.

(2007) Mol Cell 28: 434-445

Released	2008-03-18
Method	ELECTRON MICROSCOPY 12.5 Å
Organisms	Thermus thermophilus HB27 synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 7

Explore in 3D

2YWE	Download File View File

Crystal structure of LepA from Aquifex aeolicus

Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	GTP-binding protein lepA (protein)

Explore in 3D

2YWF	Download File View File

Crystal structure of GMPPNP-bound LepA from Aquifex aeolicus

Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	GTP-binding protein lepA (protein)
Unique Ligands	GNP, MG

Explore in 3D

2YWG	Download File View File

Crystal structure of GTP-bound LepA from Aquifex aeolicus

Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.94 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	GTP-binding protein LepA (protein)
Unique Ligands	GTP

Explore in 3D

2YWH	Download File View File

Crystal structure of GDP-bound LepA from Aquifex aeolicus

Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	GTP-binding protein LepA (protein)
Unique Ligands	GDP, MG

Explore in 3D

2YWK	Download File View File

Crystal structure of RRM-domain derived from human putative RNA-binding protein 11

Kawazoe, M., Takemoto, C., Kaminishi, T., Uchikubo-Kamo, T., Nishino, A., Morita, S., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Homo sapiens
Macromolecule	Putative RNA-binding protein 11 (protein)

Explore in 3D

2YWQ	Download File View File

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-15
Method	X-RAY DIFFRACTION 2.64 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribosomal subunit interface protein (protein)

Explore in 3D

2Z0I	Download File View File

Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus

Wang, H., Xie, Y., Kawazoe, M., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-05-13
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Mus musculus
Macromolecule	Delta-aminolevulinic acid dehydratase (protein)

Explore in 3D

2Z0T	Download File View File

Crystal structure of hypothetical protein PH0355

Murayama, K., Takemoto, C., Kato-Murayama, M., Kawazoe, M., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-11-13
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Putative uncharacterized protein PH0355 (protein)

Explore in 3D

2Z1B	Download File View File

Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculs

Xie, Y., Wang, H., Kawazoe, M., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirozu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-05-13
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Mus musculus
Macromolecule	Delta-aminolevulinic acid dehydratase (protein)

Explore in 3D

2ZM6	Download File View File

Crystal structure of the Thermus thermophilus 30S ribosomal subunit

Kaminishi, T., Wang, H., Kawazoe, M., Ishii, R., Schluenzen, F., Hanawa-Suetsugu, K., Wilson, D.N., Nomura, M., Takemoto, C., Shirouzu, M., Fucini, P., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-04-14
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Thermus thermophilus
Macromolecule	Unique protein chains: 20 Unique nucleic acid chains: 1
Unique Ligands	ZN

Explore in 3D

2ZUL	Download File View File

Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine

Wang, H., Kawazoe, M., Tatsuguchi, A., Naoe, C., Takemoto, C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-10-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Probable ribosomal RNA small subunit methyltransferase (protein)
Unique Ligands	SAM

Explore in 3D

2ZWV	Download File View File

Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533)

Wang, H., Kawazoe, M., Kaminishi, T., Tatsuguchi, A., Naoe, C., Terada, T., Shirouzu, M., Takemoto, C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-12-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Probable ribosomal RNA small subunit methyltransferase (protein)
Unique Ligands	SAH

Explore in 3D

3A1P	Download File View File

Structure of Ribosome maturation protein RimM and Ribosomal protein S19

Kaminishi, T., Takemoto, C., Tatsuguchi, A., Kawazoe, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2010-04-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus HB8
Macromolecule	30S ribosomal protein S19 (protein) Ribosome maturation factor rimM (protein)
Unique Ligands	UNX

1 to 25 of 28 Structures

Page 1 of 2

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.

All questions and comments will receive a response in a timely manner.

Use this form for questions about RCSB.org and RCSB PDB services.
Please attach a screenshot when reporting an issue, if possible.
To update/release your in-progress structure depositions:
access the OneDep Communication panel
For questions/corrections to specific PDB entries, including citation updates:
email deposit-help@mail.wwpdb.org

First Name

Last Name

Subject

Question, Comment, Feedback or Other

Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)

I agree to the Help Desk Privacy Policy

Optional: To help us learn more about our users, what is your:

Institution Type

Role

Main Research Interest

Thank you for providing your feedback! Someone will be in touch with you shortly. This window will automatically close in 5 seconds.

Apologies, our feedback server is currently unavailable and we are troubleshooting the issue. In the meantime, please copy and paste the below information into an email addressed to info@rcsb.org

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

Symmetry Type

SCOP Classification