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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Malyutin, A.G."

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Search Summary

This query matches 34 Structures.

Refinements

Structure Determination Methodology

experimental (34)

Scientific Name of Source Organism

	synthetic construct (30)
	Betapolyomavirus macacae (22)
	Homo sapiens (10)
	Acidianus ambivalens (1)
	Aquifex aeolicus VF5 (1)

Taxonomy

	other sequences (30)
	Monodnaviria (22)
	Eukaryota (10)
	Archaea (1)
	Bacteria (1)

Experimental Method

ELECTRON MICROSCOPY (34)

Polymer Entity Type

	Protein (34)
	DNA (30)

Refinement Resolution (Å)

	2.0 - 2.5 (1)
	2.5 - 3.0 (1)
	3.0 - 3.5 (24)
	4.0 - 4.5 (4)
	> 4.5 (4)

Release Date

	2015 - 2019 (5)
	2020 - 2024 (7)
	2025 - 2029 (22)

Enzyme Classification Name

	Hydrolases (26)
	Isomerases (22)
	Transferases (8)
	Ligases (3)
	Oxidoreductases (1)

Symmetry Type

	Cyclic (22)
	Asymmetric (10)
	Icosahedral (1)
	Octahedral (1)

AllSelected

1 to 25 of 34 Structures

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6S1M \| pdb_00006s1m	Download File View File

Human polymerase delta holoenzyme Conformer 1

Lancey, C., Hamdan, S.M., De Biasio, A.

(2020) Nat Commun 11: 1109-1109

Released	2019-12-25
Method	ELECTRON MICROSCOPY 4.27 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SF4, TTP, ZN

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6S1N \| pdb_00006s1n	Download File View File

Human polymerase delta holoenzyme Conformer 2

Lancey, C., Hamdan, S.M., De Biasio, A.

(2020) Nat Commun 11: 1109-1109

Released	2019-12-25
Method	ELECTRON MICROSCOPY 4.86 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SF4, TTP, ZN

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6S1O \| pdb_00006s1o	Download File View File

Human polymerase delta holoenzyme Conformer 3

Lancey, C., Hamdan, S.M., De Biasio, A.

(2020) Nat Commun 11: 1109-1109

Released	2019-12-25
Method	ELECTRON MICROSCOPY 8.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SF4, TTP, ZN

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6TNY \| pdb_00006tny	Download File View File

Processive human polymerase delta holoenzyme

Lancey, C., Hamdan, S.M., De Biasio, A.

(2020) Nat Commun 11: 1109-1109

Released	2019-12-18
Method	ELECTRON MICROSCOPY 3.08 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SF4, TTP, ZN

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6TNZ \| pdb_00006tnz	Download File View File

Human polymerase delta-FEN1-PCNA toolbelt

Lancey, C., Hamdan, S.M., De Biasio, A.

(2020) Nat Commun 11: 1109-1109

Released	2019-12-18
Method	ELECTRON MICROSCOPY 4.05 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	SF4, TTP, ZN

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7NV0 \| pdb_00007nv0	Download File View File

Human Pol Kappa holoenzyme with wt PCNA

Lancey, C., De Biasio, A., Hamdan, S.M.

(2021) Nat Commun 12: 6095-6095

Released	2021-11-10
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase kappa (protein) Proliferating cell nuclear antigen (protein) DNA Primer (nucleic acid) DNA Template (nucleic acid)
Unique Ligands	TTP

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7NV1 \| pdb_00007nv1	Download File View File

Human Pol Kappa holoenzyme with Ub-PCNA

Lancey, C., De Biasio, A., Hamdan, S.M.

(2021) Nat Commun 12: 6095-6095

Released	2021-11-03
Method	ELECTRON MICROSCOPY 6.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase kappa (protein) Proliferating cell nuclear antigen (protein) DNA Primer (nucleic acid) DNA Template (nucleic acid)
Unique Ligands	TTP

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7QNZ \| pdb_00007qnz	Download File View File

human Lig1-DNA-PCNA complex reconstituted in absence of ATP

Blair, K., Tehseen, M., Raducanu, V.S., Shahid, T., Lancey, C., Cruehet, R., Hamdan, S., De Biasio, A.

(2022) Nat Commun 13: 7833-7833

Released	2023-01-11
Method	ELECTRON MICROSCOPY 4.58 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA ligase 1 (protein) Proliferating cell nuclear antigen (protein) Oligo13P (nucleic acid) Oligo19ddC (nucleic acid) Oligo32 (nucleic acid)
Unique Ligands	AMP

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7QO1 \| pdb_00007qo1	Download File View File

complex of DNA ligase I and FEN1 on PCNA and DNA

Blair, K., Tehseen, M., Raducanu, V.S., Shahid, T., Lancey, C., Cruehet, R., Hamdan, S., De Biasio, A.

(2022) Nat Commun 13: 7833-7833

Released	2023-01-11
Method	ELECTRON MICROSCOPY 4.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3
Unique Ligands	AMP

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7X7M \| pdb_00007x7m	Download File View File

Lumazine Synthase from Aquifex aeolicus

Sobhy, M.A., Hamdan, S.M.

(2022) PLoS One 17: e0275487-e0275487

Released	2022-10-12
Method	ELECTRON MICROSCOPY 2.33 Å
Organisms	Aquifex aeolicus VF5
Macromolecule	6,7-dimethyl-8-ribityllumazine synthase (protein)

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7X9W \| pdb_00007x9w	Download File View File

Sulfur Oxygenase Reductase from Acidianus ambivalens

Sobhy, M.A., Hamdan, S.M.

(2022) PLoS One 17: e0275487-e0275487

Released	2022-10-12
Method	ELECTRON MICROSCOPY 2.78 Å
Organisms	Acidianus ambivalens
Macromolecule	Sulfur oxygenase/reductase (protein)
Unique Ligands	FE

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8B8T \| pdb_00008b8t	Download File View File

Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP

Blair, K., Tehseen, M., Raducanu, V.S., Shahid, T., Lancey, C., Cruehet, R., Hamdan, S., De Biasio, A.

(2022) Nat Commun 13: 7833-7833

Released	2023-01-11
Method	ELECTRON MICROSCOPY 4.2 Å
Organisms	Homo sapiens
Macromolecule	DNA ligase 1 (protein) Proliferating cell nuclear antigen (protein)

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9EVH \| pdb_00009evh	Download File View File

SV40 large T antigen assembly with DNA in presence of ADP

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.38 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) DNA (nucleic acid)
Unique Ligands	ADP

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9EVP \| pdb_00009evp	Download File View File

SV40 LTAg assembly with DNA in presence of AMPPNP and Mg2+.

Shahid, T., De Biasio, A., Clark, A., Savva, C.G.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.12 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) DNA (nucleic acid)
Unique Ligands	ANP, MG

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9EXD \| pdb_00009exd	Download File View File

SV40 LTAg assembly in presence of ATP.

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Betapolyomavirus macacae
Macromolecule	Large T antigen (protein)
Unique Ligands	ATP

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9F3T \| pdb_00009f3t	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_000, frame_010).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) DNA (nucleic acid)
Unique Ligands	ATP

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9F3U \| pdb_00009f3u	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_001, frame_010).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) DNA (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F5I \| pdb_00009f5i	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_000, frame_005).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) DNA (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F73 \| pdb_00009f73	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_002, frame_015).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F74 \| pdb_00009f74	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_000, frame_015).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F75 \| pdb_00009f75	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_000, frame_019).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F7N \| pdb_00009f7n	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_000, frame_000).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F9N \| pdb_00009f9n	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_001, frame_005).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F9O \| pdb_00009f9o	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_001, frame_015).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ATP

Explore in 3D

9F9W \| pdb_00009f9w	Download File View File

Active SV40 LTAg complex with DNA (3D variability component_001, frame_019).

Shahid, T.

(2025) Nature

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Betapolyomavirus macacae synthetic construct
Macromolecule	Large T antigen (protein) Chains: S (nucleic acid)
Unique Ligands	ADP, ATP

1 to 25 of 34 Structures

Page 1 of 2

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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

6S1M | pdb_00006s1m

6S1N | pdb_00006s1n

6S1O | pdb_00006s1o

6TNY | pdb_00006tny

6TNZ | pdb_00006tnz

7NV0 | pdb_00007nv0

7NV1 | pdb_00007nv1

7QNZ | pdb_00007qnz

7QO1 | pdb_00007qo1

7X7M | pdb_00007x7m

7X9W | pdb_00007x9w

8B8T | pdb_00008b8t

9EVH | pdb_00009evh

9EVP | pdb_00009evp

9EXD | pdb_00009exd

9F3T | pdb_00009f3t

9F3U | pdb_00009f3u

9F5I | pdb_00009f5i

9F73 | pdb_00009f73

9F74 | pdb_00009f74

9F75 | pdb_00009f75

9F7N | pdb_00009f7n

9F9N | pdb_00009f9n

9F9O | pdb_00009f9o

9F9W | pdb_00009f9w