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

233,249 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 = "Hata, 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 57 Structures.

Refinements

Structure Determination Methodology

experimental (57)

Scientific Name of Source Organism

	Homo sapiens (41)
	Bos taurus (4)
	Canis lupus familiaris (4)
	Leptolyngbya sp. O-77 (4)
	Crimean-Congo hemorrhagic fever virus strain IbAr10200 (3)
	Mus musculus (3)
	Serratia marcescens (2)
	Influenza A virus (1)
	Paenibacillus lautus NBRC 15380 (1)
	Saccharomyces cerevisiae S288C (1)

More...

Taxonomy

	Eukaryota (47)
	Bacteria (8)
	Riboviria (4)
	Adnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (54)
	ELECTRON MICROSCOPY (2)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (57)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (15)
	2.0 - 2.5 (12)
	2.5 - 3.0 (15)
	3.0 - 3.5 (6)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (12)
	2010 - 2014 (16)
	2015 - 2019 (13)
	2020 - 2024 (16)

Enzyme Classification Name

	Hydrolases (21)
	Transferases (7)
	Ligases (4)
	Oxidoreductases (4)

Symmetry Type

	Asymmetric (37)
	Cyclic (15)
	Dihedral (5)
	Octahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (20)
	Artifacts (9)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 57 Structures

Page 1 of 3

Sort by

Explore in 3D

1WRD \| pdb_00001wrd	Download File View File

Crystal structure of Tom1 GAT domain in complex with ubiquitin

Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) FEBS Lett 579: 5385-5391

Released	2005-10-11
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Target of Myb protein 1 (protein) Ubiquitin (protein)

Explore in 3D

2PZ9 \| pdb_00002pz9	Download File View File

Crystal structure of putative transcriptional regulator SCO4942 from Streptomyces coelicolor

Filippova, E.V., Chruszcz, M., Xu, X., Zheng, H., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2007) Nat Methods 4: 1019-1021

Released	2007-06-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Streptomyces coelicolor A3(2)
Macromolecule	Putative regulatory protein (protein)
Unique Ligands	SO4

Explore in 3D

2WWZ \| pdb_00002wwz	Download File View File

TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121

Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., Komander, D.

(2009) Nat Struct Mol Biol 16: 1328

Released	2009-11-24
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2 (protein) UBIQUITIN (protein)
Unique Ligands	ZN

Explore in 3D

2WX0 \| pdb_00002wx0	Download File View File

TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21

Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., Komander, D.

(2009) Nat Struct Mol Biol 16: 1328

Released	2009-11-24
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2 (protein) UBIQUITIN (protein)
Unique Ligands	ZN

Explore in 3D

2WX1 \| pdb_00002wx1	Download File View File

TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked tri-ubiquitin, P212121

Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., Komander, D.

(2009) Nat Struct Mol Biol 16: 1328

Released	2009-11-24
Method	X-RAY DIFFRACTION 3 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2 (protein) UBIQUITIN (protein)
Unique Ligands	ZN

Explore in 3D

2Y5B \| pdb_00002y5b	Download File View File

Structure of USP21 in complex with linear diubiquitin-aldehyde

Ye, Y., Akutsu, M., Reyes-Turcu, F., Enchev, R.I., Wilkinson, K.D., Komander, D.

(2011) EMBO Rep 12: 350

Released	2012-01-25
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	UBIQUITIN (protein) UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21 (protein)
Unique Ligands	SO4, ZN

Explore in 3D

2ZFY \| pdb_00002zfy	Download File View File

Crystal structure of human Otubain 1

Akutsu, M., Walker, J.R., Li, Y., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

(2009) Biochem J 418: 379-390

Released	2008-02-19
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin thioesterase OTUB1 (protein)

Explore in 3D

2ZVN \| pdb_00002zvn	Download File View File

NEMO CoZi domain incomplex with diubiquitin in P212121 space group

Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S., Dikic, I.

(2009) Cell 136: 1098-1109

Released	2009-03-24
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	NF-kappa-B essential modulator (protein) UBC protein (protein)

Explore in 3D

2ZVO \| pdb_00002zvo	Download File View File

NEMO CoZi domain in complex with diubiquitin in C2 space group

Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S., Dikic, I.

(2009) Cell 136: 1098-1109

Released	2009-03-24
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	NF-kappa-B essential modulator (protein) UBC protein (protein)

Explore in 3D

3BFO \| pdb_00003bfo	Download File View File

Crystal structure of Ig-like C2-type 2 domain of the human Mucosa-associated lymphoid tissue lymphoma translocation protein 1

Walker, J.R., Akutsu, M., Littler, D.R., Li, Y., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

To be published

Released	2007-12-11
Method	X-RAY DIFFRACTION 1.15 Å
Organisms	Homo sapiens
Macromolecule	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2) (protein)

Explore in 3D

3EBB \| pdb_00003ebb	Download File View File

PLAP/P97 complex

Walker, J.R., Qiu, L., Akutsu, M., Slessarev, Y., Amaya, M.F., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

(2010) J Biological Chem 285: 365-372

Released	2009-02-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	PHOSPHOLIPASE A2-ACTIVATING PROTEIN (protein) TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP (protein)
Unique Ligands	MG

Explore in 3D

3EBQ \| pdb_00003ebq	Download File View File

Crystal structure of human PPPDE1

Walker, J.R., Akutsu, M., Qiu, L., Li, Y., Slessarev, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Botchkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

To be published

Released	2008-11-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	MOLECULE: PPPDE1 (PERMUTED PAPAIN FOLD PEPTIDASES OF DSRNA VIRUSES AND EUKARYOTES 1), UPF0326 protein FAM152B (protein)
Unique Ligands	HG

Explore in 3D

3F89 \| pdb_00003f89	Download File View File

NEMO CoZi domain

Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S., Dikic, I.

(2009) Cell 136: 1098-1109

Released	2009-03-24
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mus musculus
Macromolecule	NF-kappa-B essential modulator (protein)

Explore in 3D

3PHU \| pdb_00003phu	Download File View File

OTU Domain of Crimean Congo Hemorrhagic Fever Virus

Akutsu, M., Ye, Y., Virdee, S., Komander, D.

(2011) Proc Natl Acad Sci U S A 108: 2228-2233

Released	2011-02-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Crimean-Congo hemorrhagic fever virus strain IbAr10200
Macromolecule	RNA-directed RNA polymerase L (protein)
Unique Ligands	GOL

Explore in 3D

3PHW \| pdb_00003phw	Download File View File

OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin

Akutsu, M., Ye, Y., Virdee, S., Komander, D.

(2011) Proc Natl Acad Sci U S A 108: 2228-2233

Released	2011-02-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Crimean-Congo hemorrhagic fever virus strain IbAr10200 Homo sapiens
Macromolecule	RNA-directed RNA polymerase L (protein) Ubiquitin-40S ribosomal protein S27a (protein)
Unique Ligands	NEH

Explore in 3D

3PHX \| pdb_00003phx	Download File View File

OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15

Akutsu, M., Ye, Y., Virdee, S., Komander, D.

(2011) Proc Natl Acad Sci U S A 108: 2228-2233

Released	2011-02-02
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Crimean-Congo hemorrhagic fever virus strain IbAr10200 Homo sapiens
Macromolecule	RNA-directed RNA polymerase L (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	ACY, NEH, ZN

Explore in 3D

3VVV \| pdb_00003vvv	Download File View File

Skich domain of NDP52

Akutsu, M., Muhlinen, N.V., Randow, F., Komander, D.

(2012) Mol Cell 48: 329-342

Released	2013-02-27
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Homo sapiens
Macromolecule	Calcium-binding and coiled-coil domain-containing protein 2 (protein)

Explore in 3D

3VVW \| pdb_00003vvw	Download File View File

NDP52 in complex with LC3C

Akutsu, M., Muhlinen, N.V., Randow, F., Komander, D.

(2012) Mol Cell 48: 329-342

Released	2013-02-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Calcium-binding and coiled-coil domain-containing protein 2 (protein) Microtubule-associated proteins 1A/1B light chain 3C (protein)

Explore in 3D

3ZRH \| pdb_00003zrh	Download File View File

Crystal structure of the Lys29, Lys33-linkage-specific TRABID OTU deubiquitinase domain reveals an Ankyrin-repeat ubiquitin binding domain (AnkUBD)

Licchesi, J.D.F., Akutsu, M., Komander, D.

(2011) Nat Struct Mol Biol 19: 62

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Homo sapiens
Macromolecule	UBIQUITIN THIOESTERASE ZRANB1 (protein)
Unique Ligands	CL, EDO

Explore in 3D

4BOP \| pdb_00004bop	Download File View File

Structure of OTUD1 OTU domain

Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.

(2013) Cell 154: 169

Released	2013-07-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	OTU DOMAIN-CONTAINING PROTEIN 1 (protein)
Unique Ligands	PO4

Explore in 3D

4BOQ \| pdb_00004boq	Download File View File

Structure of OTUD2 OTU domain

Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.

(2013) Cell 154: 169

Released	2013-07-17
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Homo sapiens
Macromolecule	UBIQUITIN THIOESTERASE OTU1 (protein)
Unique Ligands	GOL

Explore in 3D

4BOS \| pdb_00004bos	Download File View File

Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide

Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.

(2013) Cell 154: 169

Released	2013-07-24
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	OTUD2 (protein) POLYUBIQUITIN-C (protein) UBIQUITIN THIOESTERASE OTU1 (protein)
Unique Ligands	MG, NO3

Explore in 3D

4BOU \| pdb_00004bou	Download File View File

Structure of OTUD3 OTU domain

Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.

(2013) Cell 154: 169

Released	2013-07-17
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	OTU DOMAIN-CONTAINING PROTEIN 3 (protein)

Explore in 3D

4BOZ \| pdb_00004boz	Download File View File

Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin

Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.

(2013) Cell 154: 169

Released	2013-07-17
Method	X-RAY DIFFRACTION 3.03 Å
Organisms	Homo sapiens
Macromolecule	UBIQUITIN THIOESTERASE OTU1 (protein) UBIQUITIN-C (protein)
Unique Ligands	GOL