QUERY: Citation Author = "Yamamoto, J."
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Search Summary This query matches 60 Structures.
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1 to 25 of 60 Structures
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3FY4

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(6-4) Photolyase Crystal Structure

Hitomi, K., Arvai, A.S., Tainer, J.A., Getzoff, E.D.

(2009) Proc Natl Acad Sci U S A 106: 6962-6967

Released2009-04-28
Method
X-RAY DIFFRACTION 2.7 Å
Organisms
Macromolecule
Unique LigandsFAD, IMD, MES, PO4
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3UMV

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Eukaryotic Class II CPD photolyase structure reveals a basis for improved UV-tolerance in plants

Arvai, A.S., Hitomi, K., Getzoff, E.D., Tainer, J.A.

(2012) J Biological Chem 287: 12060-12069

Released2011-12-21
Method
X-RAY DIFFRACTION 1.705 Å
Organisms
Macromolecule
Unique LigandsEDO, FAD, URE
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4YM5

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Crystal structure of the human nucleosome containing 6-4PP (inside)

Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.

(2015) Sci Rep 5: 16330-16330

Released2015-12-02
Method
X-RAY DIFFRACTION 4.005 Å
Organisms
Macromolecule
Unique protein chains: 4
Unique nucleic acid chains: 2
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4YM6

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Crystal structure of the human nucleosome containing 6-4PP (outside)

Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.

(2015) Sci Rep 5: 16330-16330

Released2015-12-02
Method
X-RAY DIFFRACTION 3.514 Å
Organisms
Macromolecule
Histone H3.1 (protein)
Histone H4 (protein)
145-MER DNA (nucleic acid)
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5ZCW

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Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion

Maestre-Reyna, M., Bessho, Y.

(2018) IUCrJ 5: 608-618

Released2018-08-22
Method
X-RAY DIFFRACTION 2.7 Å
Organisms
Macromolecule
Unique LigandsACT, FAD, SO4
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5ZM0

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X-ray structure of animal-like Cryptochrome from Chlamydomonas reinhardtii

Franz, S., Ignatz, E., Wenzel, S., Zielosko, H., Gusti Ngurah Putu, E.P., Maestre-Reyna, M., Tsai, M.-D., Yamamoto, J., Mittag, M., Essen, L.-O.

(2018) Nucleic Acids Res 46: 8010-8022

Released2018-07-25
Method
X-RAY DIFFRACTION 1.6 Å
Organisms
Macromolecule
Unique LigandsCL, FAD, GOL, MES
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6FN0

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The animal-like Cryptochrome from Chlamydomonas reinhardtii in complex with 6-4 DNA

Franz, S., Ignatz, E., Wenzel, S., Zielosko, H., Yamamoto, J., Mittag, M., Essen, L.-O.

(2018) Nucleic Acids Res 46: 8010-8022

Released2018-08-01
Method
X-RAY DIFFRACTION 2.9 Å
Organisms
Macromolecule
Unique Ligands1PE, CL, FAD, GOL, MES, MG
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6FN2

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X-ray structure of animal-like Cryptochrome from Chlamydomonas reinhardtii

Franz, S., Ignatz, E., Wenzel, S., Zielosko, H., Yamamoto, J., Mittag, M., Essen, L.-O.

(2018) Nucleic Acids Res 46: 8010-8022

Released2018-08-01
Method
X-RAY DIFFRACTION 2.3 Å
Organisms
Macromolecule
Unique LigandsCL, FAD, GOL, HDF, PO4
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6FN3

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X-ray structure of animal-like Cryptochrome from Chlamydomonas reinhardtii

Franz, S., Ignatz, E., Wenzel, S., Zielosko, H., Yamamoto, J., Mittag, M., Essen, L.-O.

(2018) Nucleic Acids Res 46: 8010-8022

Released2018-08-01
Method
X-RAY DIFFRACTION 1.9 Å
Organisms
Macromolecule
Unique LigandsFAD, GOL, MES, PO4
 Explore in 3D

6R8Y

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Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 4.3 Å
Organisms
Macromolecule
Unique protein chains: 7
Unique nucleic acid chains: 2
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6R8Z

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Cryo-EM structure of NCP_THF2(-1)-UV-DDB

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 3.9 Å
Organisms
Macromolecule
Unique protein chains: 6
Unique nucleic acid chains: 2
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6R90

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Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 4.5 Å
Organisms
Macromolecule
Unique protein chains: 6
Unique nucleic acid chains: 2
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6R91

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Cryo-EM structure of NCP_THF2(-3)-UV-DDB

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 4.1 Å
Organisms
Macromolecule
Unique protein chains: 6
Unique nucleic acid chains: 2
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6R92

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Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 4.8 Å
Organisms
Macromolecule
Unique protein chains: 6
Unique nucleic acid chains: 2
 Explore in 3D

6R93

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Cryo-EM structure of NCP-6-4PP

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 4 Å
Organisms
Macromolecule
Unique protein chains: 4
Unique nucleic acid chains: 2
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6R94

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Cryo-EM structure of NCP_THF2(-3)

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released2019-06-12
Method
ELECTRON MICROSCOPY 3.5 Å
Organisms
Macromolecule
Unique protein chains: 4
Unique nucleic acid chains: 2
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7C6B

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Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate

Suzuki, M., Takahashi, Y., Saito, J., Miyagi, H., Shinohara, F.

(2021) RNA 27: 163-173

Released2020-11-25
Method
X-RAY DIFFRACTION 1.7 Å
Organisms
Macromolecule
Unique LigandsK2R, PO4
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7D7U

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Crystal structure of Ago2 MID domain in complex with 8-Br-adenosin-5'-monophosphate

Suzuki, M., Takahashi, Y., Saito, J., Miyagi, H., Shinohara, F.

(2021) RNA 27: 163-173

Released2020-11-25
Method
X-RAY DIFFRACTION 2 Å
Organisms
Macromolecule
Unique Ligands8BR
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7F8T

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Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei

Maestre-Reyna, M., Yang, C.-H., Huang, W.C., Nango, E., Gusti-Ngurah-Putu, E.-P., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Sugahara, M., Owada, S., Joti, Y., Tanaka, R., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 1.5 Å
Organisms
Macromolecule
Unique LigandsFAD, GOL, SO4
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7VIW

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Dark adapted MmCPDII during oxidized to semiquinone TR-SFX studies

Maestre-Reyna, M., Yang, C.-H., Huang, W.-C., Nango, E., Ngura Putu, E.P.G., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Hosokawa, Y., Saft, M., Emmerich, H.-J., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Royant, A., Gad, W., Pang, A.H., Chang, C.-W., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 1.74 Å
Organisms
Macromolecule
Unique LigandsFAD, SO4
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7VIX

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class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (10 ns time-point)

Maestre-Reyna, M., Yang, C.-H., Huang, W.-C., Nango, E., Ngura Putu, E.P.G., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Hosokawa, Y., Saft, M., Emmerich, H.-J., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Royant, A., Gad, W., Pang, A.H., Chang, C.-W., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 2.5 Å
Organisms
Macromolecule
Unique LigandsFAD, SO4
 Explore in 3D

7VIY

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class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (50 ns time-point)

Maestre-Reyna, M., Yang, C.-H., Huang, W.-C., Nango, E., Ngura Putu, E.P.G., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Hosokawa, Y., Saft, M., Emmerich, H.-J., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Royant, A., Gad, W., Pang, A.H., Chang, C.-W., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 2.25 Å
Organisms
Macromolecule
Unique LigandsFAD, SO4
 Explore in 3D

7VIZ

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class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (250 ns time-point)

Maestre-Reyna, M., Yang, C.-H., Huang, W.-C., Nango, E., Ngura Putu, E.P.G., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Hosokawa, Y., Saft, M., Emmerich, H.-J., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Royant, A., Gad, W., Pang, A.H., Chang, C.-W., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 2.4 Å
Organisms
Macromolecule
Unique LigandsFAD, SO4
 Explore in 3D

7VJ0

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class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (1 us time-point)

Maestre-Reyna, M., Yang, C.-H., Huang, W.-C., Nango, E., Ngura Putu, E.P.G., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Hosokawa, Y., Saft, M., Emmerich, H.-J., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Royant, A., Gad, W., Pang, A.H., Chang, C.-W., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 2.3 Å
Organisms
Macromolecule
Unique LigandsFAD, SO4
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7VJ1

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class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (10 us time-point)

Maestre-Reyna, M., Yang, C.-H., Huang, W.-C., Nango, E., Ngura Putu, E.P.G., Franz-Badur, S., Wu, W.-J., Wu, H.-Y., Wang, P.-H., Hosokawa, Y., Saft, M., Emmerich, H.-J., Liao, J.-H., Lee, C.-C., Huang, K.-F., Chang, Y.-K., Weng, J.-H., Royant, A., Gad, W., Pang, A.H., Chang, C.-W., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Yamamoto, J., Iwata, S., Essen, L.-O., Bessho, Y., Tsai, M.-D.

(2022) Nat Chem 14: 677-685

Released2022-03-09
Method
X-RAY DIFFRACTION 2.25 Å
Organisms
Macromolecule
Unique LigandsFAD, SO4
1 to 25 of 60 Structures
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