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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Hirano, H."

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Search Summary

This query matches 50 Structures.

Refinements

Structure Determination Methodology

experimental (50)

Scientific Name of Source Organism

	Mus musculus (10)
	synthetic construct (9)
	Homo sapiens (7)
	Streptococcus pyogenes (6)
	Streptococcus pyogenes serotype M1 (5)
	Moloney murine leukemia virus (4)
	Aspergillus aculeatus (3)
	Francisella tularensis subsp. novicida (3)
	Francisella tularensis subsp. novicida U112 (3)
	Mycolicibacterium mucogenicum (3)

More...

Taxonomy

	Eukaryota (25)
	Bacteria (22)
	other sequences (9)
	Riboviria (5)
	Archaea (3)
	Duplodnaviria (2)
	Eukaryota (eukaryotes) (1)

Experimental Method

	ELECTRON MICROSCOPY (26)
	X-RAY DIFFRACTION (23)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (50)
	RNA (24)
	DNA (20)
	NA-hybrid (2)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (1)
	1.5 - 2.0 (8)
	2.0 - 2.5 (9)
	2.5 - 3.0 (11)
	3.0 - 3.5 (14)
	3.5 - 4.0 (3)
	> 4.5 (2)

Release Date

	2000 - 2004 (1)
	2010 - 2014 (8)
	2015 - 2019 (14)
	2020 - 2024 (26)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (30)
	Lyases (1)

Membrane Protein Annotation

	PDBTM (7)
	OPM (6)
	MemProtMD (4)
	mpstruc (4)

Symmetry Type

	Asymmetric (44)
	Cyclic (5)
	Dihedral (1)

SCOP Classification

	All beta proteins (5)
	All alpha proteins (4)
	Small proteins (1)

AllSelected

1 to 25 of 50 Structures

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1JU8 \| pdb_00001ju8	Download File View File

Solution structure of Leginsulin, a plant hormon

Yamazaki, T., Takaoka, M., Katoh, E., Hanada, K., Sakita, M., Sakata, K., Nishiuchi, Y., Hirano, H.

(2003) Eur J Biochem 270: 1269-1276

Released	2003-06-17
Method	SOLUTION NMR
Organisms	Glycine max
Macromolecule	Leginsulin (protein)

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3AUP \| pdb_00003aup	Download File View File

Crystal structure of Basic 7S globulin from soybean

Yoshizawa, T., Shimizu, T., Taichi, M., Nishiuchi, Y., Yamabe, M., Shichijo, N., Unzai, S., Hirano, H., Sato, M., Hashimoto, H.

(2011) FEBS J 278: 1944-1954

Released	2011-04-27
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Glycine max
Macromolecule	Basic 7S globulin (protein)

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3TPM \| pdb_00003tpm	Download File View File

Crystal structure of MAL RPEL domain in complex with importin-alpha

Hirano, H., Matsuura, Y.

(2011) Biochem Biophys Res Commun 414: 373-378

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Importin subunit alpha-2 (protein) MAL (protein)

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3TPO \| pdb_00003tpo	Download File View File

Crystal structure of D192A/E396A mutant of mouse importin alpha2

Hirano, H., Matsuura, Y.

(2011) Biochem Biophys Res Commun 414: 373-378

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Importin subunit alpha-2 (protein)

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3TPQ \| pdb_00003tpq	Download File View File

Crystal structure of wild-type MAL RPEL domain in complex with five G-actins

Hirano, H., Matsuura, Y.

(2011) Biochem Biophys Res Commun 414: 373-378

Released	2011-10-12
Method	X-RAY DIFFRACTION 3.45 Å
Organisms	Mus musculus Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) MAL (protein)
Unique Ligands	ATP, CA

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3VL8 \| pdb_00003vl8	Download File View File

Crystal structure of XEG

Yoshizawa, T., Shimizu, T., Hirano, H., Sato, M., Hashimoto, H.

(2012) J Biological Chem 287: 18710-18716

Released	2012-04-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Aspergillus aculeatus
Macromolecule	Xyloglucan-specific endo-beta-1,4-glucanase A (protein)
Unique Ligands	SO4

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3VL9 \| pdb_00003vl9	Download File View File

Crystal structure of xeg-xyloglucan

Yoshizawa, T., Shimizu, T., Hirano, H., Sato, M., Hashimoto, H.

(2012) J Biological Chem 287: 18710-18716

Released	2012-04-18
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Aspergillus aculeatus
Macromolecule	Xyloglucan-specific endo-beta-1,4-glucanase A (protein)
Unique branched monosaccharides	BGC, XYS

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3VLA \| pdb_00003vla	Download File View File

Crystal structure of edgp

Yoshizawa, T., Shimizu, T., Hirano, H., Sato, M., Hashimoto, H.

(2012) J Biological Chem 287: 18710-18716

Released	2012-04-18
Method	X-RAY DIFFRACTION 0.95 Å
Organisms	Daucus carota
Macromolecule	EDGP (protein)
Unique Ligands	NAG

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3VLB \| pdb_00003vlb	Download File View File

Crystal structure of xeg-edgp

Yoshizawa, T., Shimizu, T., Hirano, H., Sato, M., Hashimoto, H.

(2012) J Biological Chem 287: 18710-18716

Released	2012-04-18
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Aspergillus aculeatus Daucus carota
Macromolecule	EDGP (protein) Xyloglucan-specific endo-beta-1,4-glucanase A (protein)

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4ZDU \| pdb_00004zdu	Download File View File

Crystal structure of importin-alpha bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein

Nakada, R., Hirano, H., Matsuura, Y.

(2015) Sci Rep 5: 15055-15055

Released	2015-10-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Mus musculus
Macromolecule	Importin subunit alpha-1 (protein) Peptide from Nucleoprotein (protein)

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4ZJ7 \| pdb_00004zj7	Download File View File

Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p

Kobayashi, J., Hirano, H., Matsuura, Y.

(2015) Biochem Biophys Res Commun 463: 309-314

Released	2015-06-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Importin subunit beta-3 (protein) Tyrosine-protein phosphatase CDC14 (protein)

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5B2O \| pdb_00005b2o	Download File View File

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGG PAM)

Hirano, H., Nishimasu, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 164: 950-961

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida U112 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (5'-D(TPGPGPTPAPTPCPGP*G)-3') (nucleic acid) Guide RNA (nucleic acid) Target DNA (nucleic acid)
Unique Ligands	ACT, CA, CL, EDO, NA, ZN

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5B2P \| pdb_00005b2p	Download File View File

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGA PAM)

Hirano, H., Nishimasu, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 164: 950-961

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida U112 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (5'-D(TPGPAPTPAPTPCPGP*G)-3') (nucleic acid) Target DNA (nucleic acid) Guide RNA (hybrid)
Unique Ligands	ACT, CA, CL, EDO, NA, ZN

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5B2Q \| pdb_00005b2q	Download File View File

Crystal structure of Francisella novicida Cas9 RHA in complex with sgRNA and target DNA (TGG PAM)

Hirano, H., Nishimasu, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 164: 950-961

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida U112 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (5'-D(TPGPGPTPAPTPCPGP*G)-3') (nucleic acid) Guide RNA (nucleic acid) Target DNA (nucleic acid)
Unique Ligands	ACT, CA, CL, EDO, NA, ZN

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5B43 \| pdb_00005b43	Download File View File

Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA

Yamano, T., Nishimasu, H., Hirano, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 165: 949-962

Released	2016-05-04
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Acidaminococcus Acidaminococcus sp. BV3L6
Macromolecule	CRISPR-associated endonuclease Cpf1 (protein) DNA (34-MER) (nucleic acid) DNA (5'-D(CPAPGPTPCPCPTPTPTPA)-3') (nucleic acid) RNA (43-MER) (nucleic acid)
Unique Ligands	EDO, NA

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5H2W \| pdb_00005h2w	Download File View File

Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340)

Hirano, H., Matsuura, Y.

(2017) J Mol Biology 429: 249-260

Released	2016-12-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Importin subunit alpha (protein) Ubiquitin-like-specific protease 1 (protein)

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5H2X \| pdb_00005h2x	Download File View File

Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172)

Hirano, H., Matsuura, Y.

(2017) J Mol Biology 429: 249-260

Released	2016-12-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Importin subunit alpha (protein) Ubiquitin-like-specific protease 1 (protein)

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5WUM \| pdb_00005wum	Download File View File

Crystal structure of mouse importin-alpha1 bound to S385-phosphorylated NLS of EBNA1

Nakada, R., Hirano, H., Matsuura, Y.

(2017) Biochem Biophys Res Commun 484: 113-117

Released	2017-01-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Human herpesvirus 4 strain B95-8 Mus musculus
Macromolecule	Epstein-Barr nuclear antigen 1 (protein) Importin subunit alpha-1 (protein)

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5WUN \| pdb_00005wun	Download File View File

Crystal structure of mouse importin-alpha1 bound to non-phosphorylated NLS of EBNA1

Nakada, R., Hirano, H., Matsuura, Y.

(2017) Biochem Biophys Res Commun 484: 113-117

Released	2017-01-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Human herpesvirus 4 strain B95-8 Mus musculus
Macromolecule	Epstein-Barr nuclear antigen 1 (protein) Importin subunit alpha-1 (protein)

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5X2G \| pdb_00005x2g	Download File View File

Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)

Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O.

(2017) Mol Cell 65: 1109-1121.e3

Released	2017-03-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Campylobacter jejuni Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	EDO

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5X2H \| pdb_00005x2h	Download File View File

Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACA PAM)

Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O.

(2017) Mol Cell 65: 1109-1121.e3

Released	2017-03-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Campylobacter jejuni Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	EDO

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6AEK \| pdb_00006aek	Download File View File

Crystal structure of ENPP1 in complex with pApG

Kato, K., Nishimasu, H., Hirano, S., Hirano, H., Ishitani, R., Nureki, O.

(2018) Nat Commun 9: 4424-4424

Released	2019-03-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d (protein)
Unique Ligands	5GP, AMP, CA, CL, EDO, NAG, ZN
Unique branched monosaccharides	MAN, NAG

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6AEL \| pdb_00006ael	Download File View File

Crystal structure of ENPP1 in complex with 3'3'-cGAMP

Kato, K., Nishimasu, H., Hirano, S., Hirano, H., Ishitani, R., Nureki, O.

(2018) Nat Commun 9: 4424-4424

Released	2019-03-06
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d (protein)
Unique Ligands	4BW, CA, CL, EDO, NAG, ZN
Unique branched monosaccharides	MAN, NAG

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7C7L \| pdb_00007c7l	Download File View File

Cryo-EM structure of the Cas12f1-sgRNA-target DNA complex

Takeda, N.S., Nakagawa, R., Okazaki, S., Hirano, H., Kobayashi, K., Kusakizako, T., Nishizawa, T., Yamashita, K., Nishimasu, H., Nureki, O.

(2021) Mol Cell 81: 558-570.e3

Released	2020-12-23
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	synthetic construct uncultured archaeon
Macromolecule	CRISPR-associated protein Cas14a.1 (protein) DNA (40-mer) (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	ZN

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7F47 \| pdb_00007f47	Download File View File

Cryo-EM structure of Rhizobium etli MprF

Nishimura, M., Hirano, H., Kobayashi, K., Gill, C.P., Phan, C.N.K., Kise, Y., Kusakizako, T., Yamashita, K., Ito, Y., Roy, H., Nishizawa, T., Nureki, O.

To be published

Released	2022-06-22
Method	ELECTRON MICROSCOPY 2.99 Å
Organisms	Rhizobium etli CFN 42
Macromolecule	Hypothetical conserved protein (protein)
Unique Ligands	1K1, PGW

1 to 25 of 50 Structures

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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

1JU8 | pdb_00001ju8

3AUP | pdb_00003aup

3TPM | pdb_00003tpm

3TPO | pdb_00003tpo

3TPQ | pdb_00003tpq

3VL8 | pdb_00003vl8

3VL9 | pdb_00003vl9

3VLA | pdb_00003vla

3VLB | pdb_00003vlb

4ZDU | pdb_00004zdu

4ZJ7 | pdb_00004zj7

5B2O | pdb_00005b2o

5B2P | pdb_00005b2p

5B2Q | pdb_00005b2q

5B43 | pdb_00005b43

5H2W | pdb_00005h2w

5H2X | pdb_00005h2x

5WUM | pdb_00005wum

5WUN | pdb_00005wun

5X2G | pdb_00005x2g

5X2H | pdb_00005x2h

6AEK | pdb_00006aek

6AEL | pdb_00006ael

7C7L | pdb_00007c7l

7F47 | pdb_00007f47