RCSB PDB: Search

2XRY \| pdb_00002xry	Download File View File

X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei

Kiontke, S., Geisselbrecht, Y., Pokorny, R., Carell, T., Batschauer, A., Essen, L.O.

(2011) EMBO J 30: 4437

Released	2011-09-14
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DEOXYRIBODIPYRIMIDINE PHOTOLYASE (protein)
Unique Ligands	FAD, GOL, SO4

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2XRZ \| pdb_00002xrz	Download File View File

X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei in complex with intact CPD-lesion

Kiontke, S., Geisselbrecht, Y., Pokorny, R., Carell, T., Batschauer, A., Essen, L.O.

(2011) EMBO J 30: 4437

Released	2011-09-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Methanosarcina mazei Go1 synthetic construct
Macromolecule	DEOXYRIBODIPYRIMIDINE PHOTOLYASE (protein) COUNTERSTRAND-OLIGONUCLEOTIDE (nucleic acid) CPD-COMPRISING OLIGONUCLEOTIDE (nucleic acid)
Unique Ligands	ACT, FAD, GOL, SO4

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4CDM \| pdb_00004cdm	Download File View File

Crystal structure of M. mazei photolyase soaked with synthetic 8-HDF

Kiontke, S., Batschauer, A., Essen, L.-O.

(2014) J Biological Chem 289: 19659

Released	2014-05-21
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DEOXYRIBODIPYRIMIDINE PHOTOLYASE (protein)
Unique Ligands	FAD, FO1, GOL, SO4

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4CDN \| pdb_00004cdn	Download File View File

Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-HDF antenna chromophore

Kiontke, S., Batschauer, A., Essen, L.-O.

(2014) J Biological Chem 289: 19659

Released	2014-05-21
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DEOXYRIBODIPYRIMIDINE PHOTOLYASE (protein)
Unique Ligands	FAD, FO1, GOL, PEG, PGE, SO4

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5HIU \| pdb_00005hiu	Download File View File

Structure of the TSC2 N-terminus

Zech, R., Kiontke, S., Kummel, D.

(2016) J Biological Chem 291: 20008-20020

Released	2016-08-10
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermochaetoides thermophila
Macromolecule	GTPase activator-like protein (protein)

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5LDD \| pdb_00005ldd	Download File View File

Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7

Kiontke, S., Kuemmel, D.

(2017) Nat Commun 8: 14034-14034

Released	2017-01-18
Method	X-RAY DIFFRACTION 2.496 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Ccz1 (protein) Mon1 (protein) Rab small monomeric GTPase-like protein (protein)
Unique Ligands	SO4

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5O86 \| pdb_00005o86	Download File View File

Mutant of claas II CPD photolyase from Methanosarcina mazei - W388F

Ignatz, E., Essen, L.-O.

(2018) Photochem Photobiol 94: 81-87

Released	2017-09-13
Method	X-RAY DIFFRACTION 1.687 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	Deoxyribodipyrimidine photolyase (protein)
Unique Ligands	FAD, GOL, SO4

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5O8D \| pdb_00005o8d	Download File View File

Mutant of class II CPD photolyase from Methanosarcina mazei - Y345F

Ignatz, E., Essen, L.-O.

(2018) Photochem Photobiol 94: 81-87

Released	2017-09-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	Deoxyribodipyrimidine photolyase (protein)
Unique Ligands	FAD, GOL, SO4

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5O8E \| pdb_00005o8e	Download File View File

Mutant of class II CPD photolyase from Methanosarcina mazei

Ignatz, E., Geisselbrecht, Y., Essen, L.-O.

(2018) Photochem Photobiol 94: 81-87

Released	2017-09-13
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	Deoxyribodipyrimidine photolyase (protein)
Unique Ligands	FAD, GOL, SO4

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6SSH \| pdb_00006ssh	Download File View File

Structure of the TSC2 GAP domain

Hansmann, P., Kiontke, S., Kummel, D.

(2020) Structure 28: 933-942.e4

Released	2020-05-27
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Thermochaetoides thermophila
Macromolecule	GTPase activator-like protein (protein)
Unique Ligands	EDO

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6ZFM \| pdb_00006zfm	Download File View File

Structure of alpha-Cobratoxin with a peptide inhibitor

Kiontke, S., Kummel, D.

(2020) J Med Chem 63: 13709-13718

Released	2020-12-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12 Naja kaouthia
Macromolecule	Alpha-cobratoxin (protein) peptide 12 (protein)
Unique Ligands	1PE, QJE

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7A0M \| pdb_00007a0m	Download File View File

TSC1 N-terminal domain

Zech, R., Kiontke, S., Kuemmel, D.

(2021) Mol Cell 81: 2705

Released	2021-05-26
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Thermochaetoides thermophila
Macromolecule	TSC1 N-terminal domain (protein)
Unique Ligands	SO4

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7A0N \| pdb_00007a0n	Download File View File

Structure of TSC1 NTD and linker domain

Fitzian, K., Kuemmel, D.

(2021) Mol Cell 81: 2705

Released	2021-05-26
Method	X-RAY DIFFRACTION 4.3 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Uncharacterized protein,Uncharacterized protein (protein)

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7F8T \| pdb_00007f8t	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Methanosarcina mazei
Macromolecule	Deoxyribodipyrimidine photolyase (protein)
Unique Ligands	FAD, GOL, SO4

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7QLA \| pdb_00007qla	Download File View File

Structure of the Rab GEF complex Mon1-Ccz1

Klink, B.U., Herrmann, E., Antoni, C., Langemeyer, L., Kiontke, S., Gatsogiannis, C., Ungermann, C., Raunser, S., Kuemmel, D.

(2022) Proc Natl Acad Sci U S A 119:

Released	2022-02-09
Method	ELECTRON MICROSCOPY 3.85 Å
Organisms	Thermochaetoides thermophila
Macromolecule	Ccz1 (protein) Vacuolar fusion protein MON1 (protein)

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7VIW \| pdb_00007viw	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VIX \| pdb_00007vix	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VIY \| pdb_00007viy	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VIZ \| pdb_00007viz	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VJ0 \| pdb_00007vj0	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VJ1 \| pdb_00007vj1	Download File View File

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

Released	2022-03-09
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VJ2 \| pdb_00007vj2	Download File View File

class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (125 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

Released	2022-03-09
Method	X-RAY DIFFRACTION 3 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, NA, SO4

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7VJ3 \| pdb_00007vj3	Download File View File

class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (400 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

Released	2022-03-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VJ4 \| pdb_00007vj4	Download File View File

class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (1 ms 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

Released	2022-03-09
Method	X-RAY DIFFRACTION 3 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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7VJ5 \| pdb_00007vj5	Download File View File

class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (5 ms 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

Released	2022-03-09
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Methanosarcina mazei Go1
Macromolecule	DNA photolyase (protein)
Unique Ligands	FAD, SO4

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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

Symmetry Type

SCOP Classification

2XRY | pdb_00002xry

2XRZ | pdb_00002xrz

4CDM | pdb_00004cdm

4CDN | pdb_00004cdn

5HIU | pdb_00005hiu

5LDD | pdb_00005ldd

5O86 | pdb_00005o86

5O8D | pdb_00005o8d

5O8E | pdb_00005o8e

6SSH | pdb_00006ssh

6ZFM | pdb_00006zfm

7A0M | pdb_00007a0m

7A0N | pdb_00007a0n

7F8T | pdb_00007f8t

7QLA | pdb_00007qla

7VIW | pdb_00007viw

7VIX | pdb_00007vix

7VIY | pdb_00007viy

7VIZ | pdb_00007viz

7VJ0 | pdb_00007vj0

7VJ1 | pdb_00007vj1

7VJ2 | pdb_00007vj2

7VJ3 | pdb_00007vj3

7VJ4 | pdb_00007vj4

7VJ5 | pdb_00007vj5