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

234,785 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 = "Miyoshi, H."

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 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Vibrio cholerae O395 (5)
	Escherichia coli (2)
	Homo sapiens (2)
	Arabidopsis thaliana (1)

Taxonomy

	Bacteria (7)
	Eukaryota (3)

Experimental Method

	ELECTRON MICROSCOPY (5)
	X-RAY DIFFRACTION (4)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (10)

Refinement Resolution (Å)

	2.0 - 2.5 (2)
	2.5 - 3.0 (3)
	3.0 - 3.5 (4)

Release Date

	2000 - 2004 (4)
	2015 - 2019 (1)
	2020 - 2024 (5)

Enzyme Classification Name

	Translocases (5)
	Oxidoreductases (2)

Membrane Protein Annotation

	PDBTM (7)
	OPM (6)
	mpstruc (5)
	MemProtMD (2)

Symmetry Type

	Asymmetric (10)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a+b) (4)
	All alpha proteins (2)
	Membrane and cell surface proteins and peptides (2)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 10 of 10 Structures

Page 1 of 1

Sort by

Explore in 3D

1IPB \| pdb_00001ipb	Download File View File

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA

Tomoo, K., Shen, X., Okabe, K., Nozoe, Y., Fukuhara, S., Morino, S., Ishida, T., Taniguchi, T., Hasegawa, H., Terashima, A., Sasaki, M., Katsuya, Y., Kitamura, K., Miyoshi, H., Ishikawa, M., Miura, K.

(2002) Biochem J 362: 539-544

Released	2002-05-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (protein)
Unique Ligands	GTA

Explore in 3D

1IPC \| pdb_00001ipc	Download File View File

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GTP

(2002) Biochem J 362: 539-544

Released	2002-05-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (protein)
Unique Ligands	MGP

Explore in 3D

1NEK \| pdb_00001nek	Download File View File

Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound

Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S.

(2003) Science 299: 700-704

Released	2003-02-25
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli
Macromolecule	Succinate dehydrogenase cytochrome b-556 subunit (protein) Succinate dehydrogenase flavoprotein subunit (protein) Succinate dehydrogenase hydrophobic membrane anchor protein (protein) Succinate dehydrogenase iron-sulfur protein (protein)
Unique Ligands	CA, CDN, EPH, F3S, FAD, FES, HEM, OAA, SF4, UQ2

Explore in 3D

1NEN \| pdb_00001nen	Download File View File

Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site

Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S.

(2003) Science 299: 700-704

Released	2003-02-25
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli
Macromolecule	Succinate dehydrogenase cytochrome b-556 subunit (protein) Succinate dehydrogenase flavoprotein subunit (protein) Succinate dehydrogenase hydrophobic membrane anchor protein (protein) Succinate dehydrogenase iron-sulfur protein (protein)
Unique Ligands	CA, CDN, DNT, EPH, F3S, FAD, FES, HEM, OAA, SF4

Explore in 3D

6NU4 \| pdb_00006nu4	Download File View File

Solution structure of the Arabidopsis thaliana RALF8 peptide

Lee, W., Markley, J.L., Frederick, R.O., Miyoshi, H., Tonelli, M., Cornilescu, G., Cornilescu, C., Sussman, M.R.

(2019) Protein Sci 28: 1115-1126

Released	2019-05-08
Method	SOLUTION NMR
Organisms	Arabidopsis thaliana
Macromolecule	Protein RALF-like 8 (protein)

Explore in 3D

7XK3 \| pdb_00007xk3	Download File View File

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 1

Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H.

(2022) Nat Commun 13: 4082-4082

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Vibrio cholerae O395
Macromolecule	Unique protein chains: 6
Unique Ligands	CA, FAD, FES, FMN, LMT, PEE, RBF

Explore in 3D

7XK4 \| pdb_00007xk4	Download File View File

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 2

Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H.

(2022) Nat Commun 13: 4082-4082

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Vibrio cholerae O395
Macromolecule	Unique protein chains: 6
Unique Ligands	CA, FAD, FES, FMN, LMT, PEE, RBF

Explore in 3D

7XK5 \| pdb_00007xk5	Download File View File

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 3

Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H.

(2022) Nat Commun 13: 4082-4082

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Vibrio cholerae O395
Macromolecule	Unique protein chains: 6
Unique Ligands	CA, FAD, FES, FMN, LMT, PEE, RBF

Explore in 3D

7XK6 \| pdb_00007xk6	Download File View File

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with aurachin D-42

Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H.

(2022) Nat Commun 13: 4082-4082

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Vibrio cholerae O395
Macromolecule	Unique protein chains: 6
Unique Ligands	0NI, CA, FAD, FES, FMN, LMT, PEE, RBF

Explore in 3D

7XK7 \| pdb_00007xk7	Download File View File

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with korormicin

Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H.

(2022) Nat Commun 13: 4082-4082

Released	2022-07-20
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Vibrio cholerae O395
Macromolecule	Unique protein chains: 6
Unique Ligands	CA, FAD, FES, FMN, IQT, LMT, PEE, RBF

1 to 10 of 10 Structures

Page 1 of 1

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.

1IPB | pdb_00001ipb

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA

1IPC | pdb_00001ipc

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GTP

1NEK | pdb_00001nek

Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound

1NEN | pdb_00001nen

Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site

6NU4 | pdb_00006nu4

Solution structure of the Arabidopsis thaliana RALF8 peptide

7XK3 | pdb_00007xk3

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 1

7XK4 | pdb_00007xk4

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 2

7XK5 | pdb_00007xk5

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 3

7XK6 | pdb_00007xk6

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with aurachin D-42

7XK7 | pdb_00007xk7

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with korormicin

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

1IPB | pdb_00001ipb

1IPC | pdb_00001ipc

1NEK | pdb_00001nek

1NEN | pdb_00001nen

6NU4 | pdb_00006nu4

7XK3 | pdb_00007xk3

7XK4 | pdb_00007xk4

7XK5 | pdb_00007xk5

7XK6 | pdb_00007xk6

7XK7 | pdb_00007xk7