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

234,136 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 = "Mizuno, N."

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

	Nitratidesulfovibrio vulgaris str. 'Miyazaki F (9)
	Bos taurus (3)
	Gallus gallus (3)
	Homo sapiens (3)
	Mus musculus (3)
	Muvirus mu (3)
	Flavobacterium sp. (2)
	Nitratidesulfovibrio vulgaris (2)
	Sphingomonas sp. A1 (2)
	Chromobacterium sp. (1)

More...

Taxonomy

	Bacteria (16)
	Eukaryota (10)
	Duplodnaviria (3)

Experimental Method

	X-RAY DIFFRACTION (20)
	ELECTRON MICROSCOPY (7)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

Protein (28)

Refinement Resolution (Å)

	1.0 - 1.5 (10)
	1.5 - 2.0 (4)
	2.0 - 2.5 (4)
	2.5 - 3.0 (2)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)
	> 4.5 (5)

Release Date

	2000 - 2004 (10)
	2005 - 2009 (3)
	2010 - 2014 (4)
	2015 - 2019 (6)
	2020 - 2024 (4)
	2025 - 2029 (1)

Enzyme Classification Name

	Oxidoreductases (9)
	Hydrolases (7)
	Translocases (2)

Membrane Protein Annotation

	PDBTM (4)
	mpstruc (2)
	MemProtMD (2)

Symmetry Type

	Asymmetric (26)
	Cyclic (4)

SCOP Classification

	Multi-domain proteins (alpha and beta) (11)
	All alpha proteins (3)
	All beta proteins (2)
	Alpha and beta proteins (a+b) (3)

AllSelected

1 to 25 of 28 Structures

Page 1 of 2

Sort by

Explore in 3D

1UBH \| pdb_00001ubh	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	CMO, F3S, FNE, MG, MPD, SF4

Explore in 3D

1UBJ \| pdb_00001ubj	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	CMO, F3S, FNE, MG, SF4

Explore in 3D

1UBK \| pdb_00001ubk	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	CMO, F3S, FNE, MG, MPD, SF4

Explore in 3D

1UBL \| pdb_00001ubl	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	CMO, F3S, FNE, MG, MPD, SF4

Explore in 3D

1UBM \| pdb_00001ubm	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	F3S, FNE, MG, MPD, SF4

Explore in 3D

1UBO \| pdb_00001ubo	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	CMO, F3S, FNE, MG, SF4

Explore in 3D

1UBR \| pdb_00001ubr	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	CMO, F3S, FNE, MG, SF4

Explore in 3D

1UBT \| pdb_00001ubt	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	F3S, FNE, MG, SF4

Explore in 3D

1UBU \| pdb_00001ubu	Download File View File

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Ogata, H., Mizoguchi, Y., Mizuno, N., Miki, K., Adachi, S., Yasuoka, N., Yagi, T., Yamauchi, O., Hirota, S., Higuchi, Y.

(2002) J Am Chem Soc 124: 11628-11635

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase Large subunit (protein) Periplasmic [NiFe] hydrogenase Small subunit (protein)
Unique Ligands	F3S, FNE, MG, SF4

Explore in 3D

1UCR \| pdb_00001ucr	Download File View File

Three-dimensional crystal structure of dissimilatory sulfite reductase D (DsrD)

Mizuno, N., Voordouw, G., Miki, K., Sarai, A., Higuchi, Y.

(2003) Structure 11: 1133-1140

Released	2003-10-14
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	Protein dsvD (protein)
Unique Ligands	SO4

Explore in 3D

1WQ2 \| pdb_00001wq2	Download File View File

Neutron Crystal Structure Of Dissimilatory Sulfite Reductase D (DsrD)

Chatake, T., Mizuno, N., Voordouw, G., Higuchi, Y., Arai, S., Tanaka, I., Niimura, N.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2306-2309

Released	2005-09-19
Method	NEUTRON DIFFRACTION 2.4 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	Protein dsvD (protein)
Unique Ligands	SO4

Explore in 3D

1WYB \| pdb_00001wyb	Download File View File

Structure of 6-aminohexanoate-dimer hydrolase

Negoro, S., Ohki, T., Shibata, N., Mizuno, N., Wakitani, Y., Tsurukame, J., Matsumoto, K., Kawamoto, I., Takeo, M., Higuchi, Y.

To be published

Released	2005-09-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Flavobacterium sp.
Macromolecule	6-aminohexanoate-dimer hydrolase (protein)

Explore in 3D

1WYC \| pdb_00001wyc	Download File View File

Structure of 6-aminohexanoate-dimer hydrolase, DN mutant

Negoro, S., Ohki, T., Shibata, N., Mizuno, N., Wakitani, Y., Tsurukame, J., Matsumoto, K., Kawamoto, I., Takeo, M., Higuchi, Y.

(2007) J Mol Biology 370: 142-156

Released	2006-02-21
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Flavobacterium sp.
Macromolecule	6-aminohexanoate-dimer hydrolase (protein)

Explore in 3D

3AH8 \| pdb_00003ah8	Download File View File

Structure of heterotrimeric G protein Galpha-q beta gamma in complex with an inhibitor YM-254890

Nishimura, A., Kitano, K., Takasaki, J., Taniguchi, M., Mizuno, N., Tago, K., Hakoshima, T., Itoh, H.

(2010) Proc Natl Acad Sci U S A 107: 13666-13671

Released	2010-07-21
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bos taurus Chromobacterium sp. Mus musculus Rattus norvegicus
Macromolecule	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1/Guanine nucleotide-binding protein G(q) subunit alpha chimeric protein (protein) YM-254890 (protein)
Unique Ligands	GDP

Explore in 3D

4BS1 \| pdb_00004bs1	Download File View File

MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition

Mizuno, N., Dramicanin, M., Mizuuchi, M., Adam, J., Wang, Y., Han, Y.W., Yang, W., Steven, A.C., Mizuuchi, K., Ramon-Maiques, S.

(2013) Proc Natl Acad Sci U S A 110: E2441

Released	2013-07-03
Method	ELECTRON MICROSCOPY 18 Å
Organisms	Muvirus mu
Macromolecule	TRANSCRIPTIONAL REGULATOR (NTRC FAMILY) (protein)
Unique Ligands	ADP

Explore in 3D

4BT0 \| pdb_00004bt0	Download File View File

MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition

Mizuno, N., Dramicanin, M., Mizuuchi, M., Adam, J., Wang, Y., Han, Y.W., Yang, W., Steven, A.C., Mizuuchi, K., Ramon-Maiques, S.

(2013) Proc Natl Acad Sci U S A 110: E2441

Released	2013-07-03
Method	ELECTRON MICROSCOPY 17 Å
Organisms	Muvirus mu
Macromolecule	TRANSCRIPTIONAL REGULATOR (protein)
Unique Ligands	ADP

Explore in 3D

4BT1 \| pdb_00004bt1	Download File View File

MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition

Mizuno, N., Dramicanin, M., Mizuuchi, M., Adam, J., Wang, Y., Han, Y.W., Yang, W., Steven, A.C., Mizuuchi, K., Ramon-Maiques, S.

(2013) Proc Natl Acad Sci U S A 110: E2441

Released	2013-07-03
Method	ELECTRON MICROSCOPY 16 Å
Organisms	Muvirus mu
Macromolecule	TRANSCRIPTIONAL REGULATOR (protein)
Unique Ligands	ADP

Explore in 3D

4XIG \| pdb_00004xig	Download File View File

Crystal structure of bacterial alginate ABC transporter determined through humid air and glue-coating method

Kaneko, A., Maruyama, Y., Mizuno, N., Baba, S., Kumasaka, T., Mikami, B., Murata, K., Hashimoto, W.

(2017) J Biological Chem 292: 15681-15690

Released	2016-01-13
Method	X-RAY DIFFRACTION 3.402 Å
Organisms	Sphingomonas sp. Sphingomonas sp. A1
Macromolecule	AlgM1 (protein) AlgM2 (protein) AlgQ2 (protein) AlgS (protein)
Unique branched monosaccharides	BEM, MAW

Explore in 3D

4XTC \| pdb_00004xtc	Download File View File

Crystal structure of bacterial alginate ABC transporter in complex with alginate pentasaccharide-bound periplasmic protein

Kaneko, A., Maruyama, Y., Mizuno, N., Baba, S., Kumasaka, T., Mikami, B., Murata, K., Hashimoto, W.

(2017) J Biological Chem 292: 15681-15690

Released	2016-03-02
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Sphingomonas sp. A1
Macromolecule	AlgM1 (protein) AlgM2 (protein) AlgQ2 (protein) AlgS (protein)
Unique branched monosaccharides	BEM

Explore in 3D

5E4P \| pdb_00005e4p	Download File View File

X-ray Crystal Structure Analysis of Magnetically Oriented Microcrystals of Lysozyme at 1.8 angstrom Resolution

Tsukui, S., Kimura, F., Garman, E.F., Baba, S., Mizuno, N., Mikami, B., Kimura, T.

(2016) J Appl Crystallogr 49: 457-461

Released	2016-08-31
Method	X-RAY DIFFRACTION 1.792 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)

Explore in 3D

5HNC \| pdb_00005hnc	Download File View File

Synchrotron X-ray single crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels

Tsukui, S., Kimura, F., Kusaka, K., Baba, S., Mizuno, N., Kimura, T.

(2016) Acta Crystallogr D Struct Biol 72: 823-829

Released	2016-07-20
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)

Explore in 3D

5HNL \| pdb_00005hnl	Download File View File

In-house X-ray single crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels

Tsukui, S., Kimura, F., Kusaka, K., Baba, S., Mizuno, N., Kimura, T.

(2016) Acta Crystallogr D Struct Biol 72: 823-829

Released	2016-07-20
Method	X-RAY DIFFRACTION 2.424 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)

Explore in 3D

6R9T \| pdb_00006r9t	Download File View File

Cryo-EM structure of autoinhibited human talin-1

Dedden, D., Schumacher, S., Zacharias, M., Biertumpfel, C., Mizuno, N.

(2019) Cell 179: 120-131.e13

Released	2019-10-16
Method	ELECTRON MICROSCOPY 6.2 Å
Organisms	Homo sapiens
Macromolecule	Talin-1 (protein)

Explore in 3D

7NWL \| pdb_00007nwl	Download File View File

Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin and TS2/16 Fv-clasp

Schumacher, S., Dedden, D., Vazquez Nunez, R., Matoba, K., Takagi, J., Biertumpfel, C., Mizuno, N.

(2021) Sci Adv 7:

Released	2021-06-02
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Integrin alpha-5 (protein) Integrin beta-1 (protein) Isoform 1 of Fibronectin (protein) TS2/16 VH(S112C)-SARAH Chimera (protein) TS2/16 VL-SARAH(S37C) Chimera (protein)
Unique Ligands	MN
Unique branched monosaccharides	BMA, MAN, NAG

Explore in 3D

7NXD \| pdb_00007nxd	Download File View File

Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation

Schumacher, S., Dedden, D., Vazquez Nunez, R., Matoba, K., Takagi, J., Biertumpfel, C., Mizuno, N.

(2021) Sci Adv 7:

Released	2021-08-25
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Homo sapiens
Macromolecule	Integrin alpha-5 (protein) Integrin beta-1 (protein)
Unique Ligands	CA, MG, NAG
Unique branched monosaccharides	BMA, MAN, NAG

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.

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

1UBH | pdb_00001ubh

1UBJ | pdb_00001ubj

1UBK | pdb_00001ubk

1UBL | pdb_00001ubl

1UBM | pdb_00001ubm

1UBO | pdb_00001ubo

1UBR | pdb_00001ubr

1UBT | pdb_00001ubt

1UBU | pdb_00001ubu

1UCR | pdb_00001ucr

1WQ2 | pdb_00001wq2

1WYB | pdb_00001wyb

1WYC | pdb_00001wyc

3AH8 | pdb_00003ah8

4BS1 | pdb_00004bs1

4BT0 | pdb_00004bt0

4BT1 | pdb_00004bt1

4XIG | pdb_00004xig

4XTC | pdb_00004xtc

5E4P | pdb_00005e4p

5HNC | pdb_00005hnc

5HNL | pdb_00005hnl

6R9T | pdb_00006r9t

7NWL | pdb_00007nwl

7NXD | pdb_00007nxd