RCSB PDB: Search

3CUL \| pdb_00003cul	Download File View File

Aminoacyl-tRNA synthetase ribozyme

Xiao, H., Murakami, H., Suga, H., Ferre-D'Amare, A.R.

(2008) Nature 454: 358-361

Released	2008-06-24
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) RNA (92-MER) (nucleic acid)
Unique Ligands	K, MG

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3CUN \| pdb_00003cun	Download File View File

Aminoacyl-tRNA synthetase ribozyme

Xiao, H., Murakami, H., Suga, H., Ferre-D'Amare, A.R.

(2008) Nature 454: 358-361

Released	2008-06-24
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) RNA (92-MER) (nucleic acid)
Unique Ligands	CO, K, MG

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3WG7 \| pdb_00003wg7	Download File View File

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

(2014) Nat Methods 11: 734-736

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, ZN

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4UB6 \| pdb_00004ub6	Download File View File

Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser

Suga, M., Akita, F., Hirata, K., Ueno, G., Murakami, H., Nakajima, Y., Shimizu, T., Yamashita, K., Yamamoto, M., Ago, H., Shen, J.R.

(2015) Nature 517: 99-103

Released	2014-12-03
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, FE2, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, SQD, UNL

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4UB8 \| pdb_00004ub8	Download File View File

Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser

Suga, M., Akita, F., Hirata, K., Ueno, G., Murakami, H., Nakajima, Y., Shimizu, T., Yamashita, K., Yamamoto, M., Ago, H., Shen, J.R.

(2015) Nature 517: 99-103

Released	2014-12-03
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, FE2, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, SQD, UNL

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5B56 \| pdb_00005b56	Download File View File

Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex

Miyatake, H., Sanjoh, A., Matusda, G., Murakami, T., Murakami, H., Hagiwara, K., Yokoyama, M., Sato, H., Miyamoto, Y., Dohmae, N., Aida, Y.

(2016) J Mol Biology 428: 2744-2757

Released	2016-06-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	HIV-1 M:B_89.6 Mus musculus
Macromolecule	Importin subunit alpha-1 (protein) Protein Vpr (protein)

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5X19 \| pdb_00005x19	Download File View File

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5X1B \| pdb_00005x1b	Download File View File

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5X1F \| pdb_00005x1f	Download File View File

CO bound cytochrome c oxidase without pump laser irradiation at 278K

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5Y5F \| pdb_00005y5f	Download File View File

Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray

Tosha, T., Nomura, T., Nishida, T., Ueno, G., Murakami, H., Yamashita, K., Hirata, K., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5G \| pdb_00005y5g	Download File View File

Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray

Tosha, T., Nomura, T., Nishida, T., Ueno, G., Murakami, H., Yamashita, K., Hirata, K., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 1.36 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5H \| pdb_00005y5h	Download File View File

SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA

Tosha, T., Nomura, T., Nishida, T., Yamagiwa, R., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Yamashita, A., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5I \| pdb_00005y5i	Download File View File

Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

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5Y5J \| pdb_00005y5j	Download File View File

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM

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5Y5K \| pdb_00005y5k	Download File View File

Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	HEM, NO

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5Y5L \| pdb_00005y5l	Download File View File

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state)

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2017-12-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	HEM

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5Y5M \| pdb_00005y5m	Download File View File

SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)

Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.

(2017) Nat Commun 8: 1585-1585

Released	2018-08-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	HEM

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7DVO \| pdb_00007dvo	Download File View File

Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL

Nomura, T., Kimura, T., Kanematsu, Y., Yamashita, K., Hirata, K., Ueno, G., Murakami, H., Hisano, T., Yamagiwa, R., Takeda, H., Gopalasingam, C., Yuki, K., Kousaka, R., Yanagasawa, S., Shoji, O., Kumasaka, T., Takano, Y., Ago, H., Yamamoto, M., Sugimoto, H., Tosha, T., Kubo, M., Shiro, Y.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-05-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Fusarium oxysporum
Macromolecule	NADP nitrous oxide-forming nitric oxide reductase (protein)
Unique Ligands	GOL, HEM, NO

3CUL | pdb_00003cul

Aminoacyl-tRNA synthetase ribozyme

3CUN | pdb_00003cun

Aminoacyl-tRNA synthetase ribozyme

3WG7 | pdb_00003wg7

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

4UB6 | pdb_00004ub6

Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser

4UB8 | pdb_00004ub8

Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser

5B56 | pdb_00005b56

Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex

5X19 | pdb_00005x19

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

5X1B | pdb_00005x1b

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

5X1F | pdb_00005x1f

CO bound cytochrome c oxidase without pump laser irradiation at 278K

5Y5F | pdb_00005y5f

Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray

5Y5G | pdb_00005y5g

Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray

5Y5H | pdb_00005y5h

SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA

5Y5I | pdb_00005y5i

Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data

5Y5J | pdb_00005y5j

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)

5Y5K | pdb_00005y5k

Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data

5Y5L | pdb_00005y5l

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state)

5Y5M | pdb_00005y5m

SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)

7DVO | pdb_00007dvo

Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL

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Scientific Name of Source Organism

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Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

3CUL | pdb_00003cul

3CUN | pdb_00003cun

3WG7 | pdb_00003wg7

4UB6 | pdb_00004ub6

4UB8 | pdb_00004ub8

5B56 | pdb_00005b56

5X19 | pdb_00005x19

5X1B | pdb_00005x1b

5X1F | pdb_00005x1f

5Y5F | pdb_00005y5f

5Y5G | pdb_00005y5g

5Y5H | pdb_00005y5h

5Y5I | pdb_00005y5i

5Y5J | pdb_00005y5j

5Y5K | pdb_00005y5k

5Y5L | pdb_00005y5l

5Y5M | pdb_00005y5m

7DVO | pdb_00007dvo