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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "H4C2"

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Search Summary

This query matches 38 Structures.

Refinements

Structure Determination Methodology

experimental (38)

Scientific Name of Source Organism

	Homo sapiens (38)
	synthetic construct (23)
	Mus musculus (4)
	Xenopus laevis (4)

Taxonomy

	Eukaryota (38)
	other sequences (23)
	Eukaryota (eukaryotes) (2)

Experimental Method

	ELECTRON MICROSCOPY (36)
	X-RAY DIFFRACTION (2)

Polymer Entity Type

	Protein (38)
	DNA (36)

Refinement Resolution (Å)

	2.0 - 2.5 (4)
	2.5 - 3.0 (2)
	3.0 - 3.5 (21)
	3.5 - 4.0 (6)
	4.0 - 4.5 (4)
	> 4.5 (1)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (1)
	2020 - 2024 (22)
	2025 - 2029 (14)

Enzyme Classification Name

	Transferases (19)
	Lyases (7)
	Hydrolases (3)
	Ligases (1)
	Oxidoreductases (1)

Symmetry Type

	Asymmetric (22)
	Cyclic (16)

SCOP Classification

All beta proteins (1)

AllSelected

1 to 25 of 38 Structures

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3DB3 \| pdb_00003db3	Download File View File

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide

Walker, J.R., Avvakumov, G.V., Xue, S., Dong, A., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

(2011) J Biological Chem 286: 24300-24311

Released	2008-09-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase UHRF1 (protein) Trimethylated histone H3-K9 peptide (protein)

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3R93 \| pdb_00003r93	Download File View File

Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide

Li, J., Li, Z., Ruan, J., Xu, C., Tong, Y., Pan, P.W., Tempel, W., Crombet, L., Min, J., Zang, J., Structural Genomics Consortium (SGC)

(2011) PLoS One 6: e25104-e25104

Released	2011-04-06
Method	X-RAY DIFFRACTION 2.057 Å
Organisms	Homo sapiens
Macromolecule	H3K9Me3 peptide (protein) M-phase phosphoprotein 8 (protein)
Unique Ligands	UNX

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6X59 \| pdb_00006x59	Download File View File

The mouse cGAS catalytic domain binding to human assembled nucleosome

Pengbiao, X., Pingwei, L., Baoyu, Z.

(2020) Nature 587: 673-677

Released	2020-09-16
Method	ELECTRON MICROSCOPY 2.98 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	ZN

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6XJD \| pdb_00006xjd	Download File View File

Two mouse cGAS catalytic domain binding to human assembled nucleosome

Xu, P., Li, P., Zhao, B.

(2020) Nature 587: 673-677

Released	2020-09-16
Method	ELECTRON MICROSCOPY 6.8 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7JO9 \| pdb_00007jo9	Download File View File

1:1 cGAS-nucleosome complex

Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q.

(2020) Science 370: 450-454

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens Mus musculus synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7JOA \| pdb_00007joa	Download File View File

2:1 cGAS-nucleosome complex

Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q.

(2020) Science 370: 450-454

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens Mus musculus synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7JZV \| pdb_00007jzv	Download File View File

Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome

Witus, S.R., Burrell, A.L., Hansen, J.M., Farrell, D.P., Dimaio, F., Kollman, J.M., Klevit, R.E.

(2021) Nat Struct Mol Biol 28: 268-277

Released	2021-02-17
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7TAN \| pdb_00007tan	Download File View File

Structure of VRK1 C-terminal tail bound to nucleosome core particle

Spangler, C.J., Budziszewski, G.R., McGinty, R.K.

(2022) Nucleic Acids Res 50: 4355-4371

Released	2022-05-04
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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7U50 \| pdb_00007u50	Download File View File

APE1 bound to a nucleosome core particle with AP-site at SHL-6

Weaver, T.M., Freudenthal, B.D.

(2022) Nat Commun 13: 5390-5390

Released	2022-09-07
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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7U51 \| pdb_00007u51	Download File View File

Nucleosome core particle with AP-site at SHL-6

Freudenthal, B.D., Weaver, T.M.

(2022) Nat Commun 13: 5390-5390

Released	2022-09-07
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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7U52 \| pdb_00007u52	Download File View File

nucleosome core particle with AP-site at SHL-6.5

Freudenthal, B.D., Weaver, T.M.

(2022) Nat Commun 13: 5390-5390

Released	2022-09-07
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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7U53 \| pdb_00007u53	Download File View File

Nucleosome core particle with AP-site at SHL0

Freudenthal, B.D., Weaver, T.M.

(2022) Nat Commun 13: 5390-5390

Released	2022-09-07
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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7UV9 \| pdb_00007uv9	Download File View File

KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate

Spangler, C.J., Skrajna, A., Foley, C.A., Budziszewski, G.R., Azzam, D.N., James, L.I., Frye, S.V., McGinty, R.K.

(2023) Nat Chem Biol 19: 624-632

Released	2023-02-22
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	FE, OH0

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8JLB \| pdb_00008jlb	Download File View File

Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant

Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Takizawa, Y., Kurumizaka, H.

(2023) Nucleic Acids Res 51: 10364-10374

Released	2023-10-04
Method	ELECTRON MICROSCOPY 2.36 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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8JLD \| pdb_00008jld	Download File View File

Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail

Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Takizawa, Y., Kurumizaka, H.

(2023) Nucleic Acids Res 51: 10364-10374

Released	2023-10-04
Method	ELECTRON MICROSCOPY 2.48 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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8OL1 \| pdb_00008ol1	Download File View File

cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure)

Xu, P.B., Ablasser, A.

(2024) Nature 627: 873-879

Released	2024-02-14
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8VMJ \| pdb_00008vmj	Download File View File

H3K4me3 nucleosome bound to PRC2_AJ119-450

Cookis, T., Nogales, E.

(2025) Nat Struct Mol Biol 32: 393-404

Released	2025-01-15
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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8VMN \| pdb_00008vmn	Download File View File

H3K4me3 nucleosome bound to PRC2_AJ1-450

Cookis, T., Nogales, E.

(2025) Nat Struct Mol Biol 32: 393-404

Released	2025-01-22
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens Xenopus laevis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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8VO0 \| pdb_00008vo0	Download File View File

H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged

Cookis, T., Nogales, E.

(2025) Nat Struct Mol Biol 32: 393-404

Released	2025-01-22
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens Xenopus laevis
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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8VOB \| pdb_00008vob	Download File View File

H3K36me3-modified nucleosome bound to PRC2_AJ1-450

Cookis, T., Nogales, E.

(2025) Nat Struct Mol Biol 32: 393-404

Released	2025-01-15
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

Explore in 3D

8VWS \| pdb_00008vws	Download File View File

Nucleosome containing 8oxoG at SHL-6

Weaver, T.M., Ling, J.A., Freudenthal, B.D.

(2024) Nat Commun 15: 10722-10722

Released	2024-10-30
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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8VWT \| pdb_00008vwt	Download File View File

OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map)

Weaver, T.M., Ling, J.A., Freudenthal, B.D.

(2024) Nat Commun 15: 10722-10722

Released	2024-10-30
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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8VWU \| pdb_00008vwu	Download File View File

Nucleosome containing 8oxoG at SHL4

Weaver, T.M., Ling, J.A., Freudenthal, B.D.

(2024) Nat Commun 15: 10722-10722

Released	2024-10-30
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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8VWV \| pdb_00008vwv	Download File View File

OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map)

Weaver, T.M., Ling, J.A., Freudenthal, B.D.

(2024) Nat Commun 15: 10722-10722

Released	2024-10-30
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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8X7I \| pdb_00008x7i	Download File View File

Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy

Ai, H.S., Tong, Z.B., Deng, Z.H., Pan, M., Liu, L.

(2024) bioRxiv

Released	2024-08-07
Method	ELECTRON MICROSCOPY 3.27 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 8 Unique nucleic acid chains: 2
Unique Ligands	ZN

1 to 25 of 38 Structures

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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

3DB3 | pdb_00003db3

3R93 | pdb_00003r93

6X59 | pdb_00006x59

6XJD | pdb_00006xjd

7JO9 | pdb_00007jo9

7JOA | pdb_00007joa

7JZV | pdb_00007jzv

7TAN | pdb_00007tan

7U50 | pdb_00007u50

7U51 | pdb_00007u51

7U52 | pdb_00007u52

7U53 | pdb_00007u53

7UV9 | pdb_00007uv9

8JLB | pdb_00008jlb

8JLD | pdb_00008jld

8OL1 | pdb_00008ol1

8VMJ | pdb_00008vmj

8VMN | pdb_00008vmn

8VO0 | pdb_00008vo0

8VOB | pdb_00008vob

8VWS | pdb_00008vws

8VWT | pdb_00008vwt

8VWU | pdb_00008vwu

8VWV | pdb_00008vwv

8X7I | pdb_00008x7i