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232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Denk, T."

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Search Summary

This query matches 27 Structures.

Refinements

Structure Determination Methodology

experimental (27)

Scientific Name of Source Organism

	Homo sapiens (13)
	Thermochaetoides thermophila DSM 1495 (12)
	Severe acute respiratory syndrome coronavirus 2 (9)
	Saccharomyces cerevisiae (2)

Taxonomy

	Eukaryota (27)
	Riboviria (9)

Experimental Method

ELECTRON MICROSCOPY (27)

Polymer Entity Type

	Protein (27)
	RNA (25)

Refinement Resolution (Å)

	2.0 - 2.5 (4)
	2.5 - 3.0 (16)
	3.0 - 3.5 (7)

Release Date

	2020 - 2024 (26)
	2025 - 2029 (1)

Enzyme Classification Name

	Transferases (19)
	Hydrolases (9)
	Lyases (12)

Symmetry Type

	Asymmetric (25)
	Cyclic (2)

SCOP Classification

All beta proteins (4)

AllSelected

1 to 25 of 27 Structures

Page 1 of 2

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Explore in 3D

6ZLW	Download File View File

SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-07-29
Method	ELECTRON MICROSCOPY 2.6 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 35 Unique nucleic acid chains: 1
Unique Ligands	ZN

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6ZM7	Download File View File

SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-07-29
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 81 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

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6ZME	Download File View File

SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 83 Unique nucleic acid chains: 5
Unique Ligands	ADP, MG, SF4, ZN

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6ZMI	Download File View File

SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-08-19
Method	ELECTRON MICROSCOPY 2.6 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 81 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

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6ZMO	Download File View File

SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-08-19
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 82 Unique nucleic acid chains: 6
Unique Ligands	MG, ZN

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6ZMT	Download File View File

SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-08-19
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 34 Unique nucleic acid chains: 1
Unique Ligands	ZN

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6ZN5	Download File View File

SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 35 Unique nucleic acid chains: 1
Unique Ligands	ZN

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6ZON	Download File View File

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 47 Unique nucleic acid chains: 1
Unique Ligands	ZN

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6ZP4	Download File View File

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2

Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.

(2020) Science 369: 1249-1255

Released	2020-07-29
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Unique protein chains: 52 Unique nucleic acid chains: 2
Unique Ligands	GTP, MG, ZN

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6ZVH	Download File View File

EDF1-ribosome complex

Best, K.M., Denk, T., Cheng, J., Thoms, M., Berninghausen, O., Beckmann, R.

(2020) Elife 9:

Released	2020-08-19
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 35 Unique nucleic acid chains: 2
Unique Ligands	MG, ZN

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6ZVI	Download File View File

Mbf1-ribosome complex

Best, K.M., Denk, T., Cheng, J., Thoms, M., Berninghausen, O., Beckmann, R.

(2020) Elife 9:

Released	2020-09-09
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 34 Unique nucleic acid chains: 4
Unique Ligands	ZN

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8PTW	Download File View File

Chaetomium thermophilum Rix1-complex

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.91 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Pre-rRNA-processing protein IPI3 (protein) Pre-rRNA-processing protein RIX1 (protein)

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8PUW	Download File View File

Chaetomium thermophilum Las1-Grc3-complex

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 3.01 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Las1 (protein) Polynucleotide 5'-hydroxyl-kinase GRC3 (protein)

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8PV1	Download File View File

Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.56 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 54 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

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8PV2	Download File View File

Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.63 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 53 Unique nucleic acid chains: 3
Unique Ligands	GTP, MG, ZN

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8PV3	Download File View File

Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 54 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

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8PV4	Download File View File

Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 59 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

Explore in 3D

8PV5	Download File View File

Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 50 Unique nucleic acid chains: 3
Unique Ligands	GTP, MG, ZN

Explore in 3D

8PV6	Download File View File

Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.94 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 57 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

Explore in 3D

8PV7	Download File View File

Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-11-15
Method	ELECTRON MICROSCOPY 2.12 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 54 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

Explore in 3D

8PV8	Download File View File

Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2024-01-10
Method	ELECTRON MICROSCOPY 2.91 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 55 Unique nucleic acid chains: 3
Unique Ligands	GTP, MG, ZN

Explore in 3D

8PVK	Download File View File

Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-12-06
Method	ELECTRON MICROSCOPY 2.55 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 55 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

Explore in 3D

8PVL	Download File View File

Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure

Thoms, M., Cheng, J., Denk, T., Berninghausen, O., Beckmann, R.

(2023) EMBO Rep 24: e57984-e57984

Released	2023-12-06
Method	ELECTRON MICROSCOPY 2.19 Å
Organisms	Thermochaetoides thermophila DSM 1495
Macromolecule	Unique protein chains: 53 Unique nucleic acid chains: 4
Unique Ligands	GTP, MG, ZN

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8RL2	Download File View File

Human pre-60S - State 5

Thoms, M., Denk, T., Beckmann, R.

To be published

Released	2025-01-15
Method	ELECTRON MICROSCOPY 2.84 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 3
Unique Ligands	GDP, GTP, MG, ZN

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8YOO	Download File View File

Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline

Li, X., Wang, M., Denk, T., Cheng, J.

(2024) Nat Commun 15: 5481-5481

Released	2024-07-10
Method	ELECTRON MICROSCOPY 2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 77 Unique nucleic acid chains: 4
Unique Ligands	MG, T1C, ZN

1 to 25 of 27 Structures

Page 1 of 2

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