RCSB PDB: Search

3WXQ \| pdb_00003wxq	Download File View File

Serial femtosecond X-ray structure of human fatty acid-binding protein type-3 (FABP3) in complex with stearic acid (C18:0) determined using X-ray free-electron laser at SACLA

Mizohata, E., Suzuki, M., Kakinouchi, K., Sugiyama, S., Murata, M., Sugahara, M., Nango, E., Tanaka, T., Tanaka, R., Tono, K., Song, C., Hatsui, T., Joti, Y., Yabashi, M., Iwata, S.

(2015) Nat Methods 12: 61-63

Released	2014-11-05
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Fatty acid-binding protein, heart (protein)
Unique Ligands	STE

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4YSA \| pdb_00004ysa	Download File View File

Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, NA

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4YSC \| pdb_00004ysc	Download File View File

Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CL, CU

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4YSD \| pdb_00004ysd	Download File View File

Room temperature structure of copper nitrite reductase from Geobacillus thermodenitrificans

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	ACY, CU

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4YSE \| pdb_00004yse	Download File View File

High resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	ACY, CU, MPD

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4YSO \| pdb_00004yso	Download File View File

Copper nitrite reductase from Geobacillus thermodenitrificans - 0.064 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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4YSP \| pdb_00004ysp	Download File View File

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 8.32 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diedrichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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4YSQ \| pdb_00004ysq	Download File View File

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 8.38 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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4YSR \| pdb_00004ysr	Download File View File

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.6 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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4YSS \| pdb_00004yss	Download File View File

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.7 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diedrichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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4YST \| pdb_00004yst	Download File View File

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 24.9 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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4YSU \| pdb_00004ysu	Download File View File

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 25.0 MGy

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, MPD, SO4

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5D4H \| pdb_00005d4h	Download File View File

High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	ACY, CU, GOL, NO2

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5D4I \| pdb_00005d4i	Download File View File

Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU, NO2

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5D4J \| pdb_00005d4j	Download File View File

Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	ACY, CL, CU, GOL

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5F7A \| pdb_00005f7a	Download File View File

Nitrite complex structure of copper nitrite reductase from Alcaligenes faecalis determined at 293 K

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU, NO2

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5F7B \| pdb_00005f7b	Download File View File

Resting state structure of CuNiR form Alcaligenes faecalis determined at 293 K

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU

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5Y7F \| pdb_00005y7f	Download File View File

Crystal structure of catalytic domain of UGGT (UDP-bound form) from Thermomyces dupontii

Satoh, T., Song, C., Zhu, T., Toshimori, T., Murata, K., Hayashi, Y., Kamikubo, H., Uchihashi, T., Kato, K.

(2017) Sci Rep 7: 12142-12142

Released	2017-09-27
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Thermomyces dupontii
Macromolecule	UGGT (protein)
Unique Ligands	CA, TRS, UDP

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5Y7O \| pdb_00005y7o	Download File View File

Crystal structure of folding sensor region of UGGT from Thermomyces dupontii

Satoh, T., Song, C., Zhu, T., Toshimori, T., Murata, K., Hayashi, Y., Kamikubo, H., Uchihashi, T., Kato, K.

(2017) Sci Rep 7: 12142-12142

Released	2017-09-27
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Thermomyces dupontii
Macromolecule	UGGT (protein)

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6IUK \| pdb_00006iuk	Download File View File

Cryo-EM structure of Murine Norovirus capsid

Song, C., Miyazaki, N., Iwasaki, K., Katayama, K., Murata, K.

(2020) PLoS Pathog 16: e1008619-e1008619

Released	2020-02-26
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Murine norovirus GV/NIH-2410/2005/USA
Macromolecule	Major capsid protein VP1 (protein)

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6KAD \| pdb_00006kad	Download File View File

Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii

Sheng, X., Watanabe, A., Li, A.J., Kim, E., Song, C., Murata, K., Song, D.F., Minagawa, J., Liu, Z.F.

(2019) Nat Plants 5: 1320-1330

Released	2019-10-23
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Unique protein chains: 23
Unique Ligands	BCR, BCT, CHL, CL, CLA, DGD, FE2, HEM, LHG, LMG, LUT, NEX, OEX, PHO, PL9, SQD, XAT

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7E55 \| pdb_00007e55	Download File View File

Cryo-EM structure of alpha 7 homo-tetradecamer

Song, C., Murata, K.

(2021) Int J Mol Sci 22:

Released	2021-05-05
Method	ELECTRON MICROSCOPY 5.9 Å
Organisms	Homo sapiens
Macromolecule	Proteasome subunit alpha type-3 (protein)

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7FG2 \| pdb_00007fg2	Download File View File

Minor cryo-EM structure of S protein trimer of SARS-CoV2 with K-874A VHH, composite map

Song, C., Murata, K., Katayama, K.

(2021) PLoS Pathog 17: e1009542-e1009542

Released	2021-09-29
Method	ELECTRON MICROSCOPY 4.4 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	K-874A VHH (protein) Spike glycoprotein (protein)

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7FG3 \| pdb_00007fg3	Download File View File

Major cryo-EM structure of S protein trimer of SARS-CoV2 with K-874, composite map

Song, C., Katayama, K., Murata, K.

(2021) PLoS Pathog 17: e1009542-e1009542

Released	2021-09-29
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	K-874A VHH (protein) Spike glycoprotein (protein)

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7FG7 \| pdb_00007fg7	Download File View File

Cryo-EM structure of S protein trimer of SARS-CoV2

Song, C., Murata, K., Katayama, K.

(2021) PLoS Pathog 17: e1009542-e1009542

Released	2021-09-29
Method	ELECTRON MICROSCOPY 6.9 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)

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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

3WXQ | pdb_00003wxq

4YSA | pdb_00004ysa

4YSC | pdb_00004ysc

4YSD | pdb_00004ysd

4YSE | pdb_00004yse

4YSO | pdb_00004yso

4YSP | pdb_00004ysp

4YSQ | pdb_00004ysq

4YSR | pdb_00004ysr

4YSS | pdb_00004yss

4YST | pdb_00004yst

4YSU | pdb_00004ysu

5D4H | pdb_00005d4h

5D4I | pdb_00005d4i

5D4J | pdb_00005d4j

5F7A | pdb_00005f7a

5F7B | pdb_00005f7b

5Y7F | pdb_00005y7f

5Y7O | pdb_00005y7o

6IUK | pdb_00006iuk

6KAD | pdb_00006kad

7E55 | pdb_00007e55

7FG2 | pdb_00007fg2

7FG3 | pdb_00007fg3

7FG7 | pdb_00007fg7