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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "RPD3L1"

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Search Summary

This query matches 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

	Homo sapiens (9)
	synthetic construct (1)

Taxonomy

	Eukaryota (9)
	other sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (8)
	X-RAY DIFFRACTION (1)

Polymer Entity Type

Protein (9)

Refinement Resolution (Å)

	3.0 - 3.5 (3)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (4)

Release Date

	2015 - 2019 (1)
	2020 - 2024 (8)

Enzyme Classification Name

Hydrolases (9)

Symmetry Type

	Asymmetric (6)
	Cyclic (2)
	Dihedral (1)

AllSelected

1 to 9 of 9 Structures

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Explore in 3D

5ICN \| pdb_00005icn	Download File View File

HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4

Millard, C.J., Robertson, N.S., Watson, P.J., Jameson, A.G., Schwabe, J.W.R.

(2016) Nat Commun 7: 11262-11262

Released	2016-05-11
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	GLY-ALA-6A0-ARG-HIS (protein) Histone deacetylase 1 (protein) Metastasis-associated protein MTA1 (protein)
Unique Ligands	IHP, K, ZN

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6Z2J \| pdb_00006z2j	Download File View File

The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

Fairall, L., Saleh, A., Ragan, T.J., Millard, C.J., Savva, C.G., Schwabe, J.W.R.

(2020) Nat Commun 11: 3252-3252

Released	2020-07-08
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens
Macromolecule	Deoxynucleotidyltransferase terminal-interacting protein 1 (protein) Histone deacetylase 1 (protein) Mitotic deacetylase-associated SANT domain protein (protein)
Unique Ligands	IHP, K, ZN

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6Z2K \| pdb_00006z2k	Download File View File

The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

Fairall, L., Saleh, A., Ragan, T.J., Millard, C.J., Savva, C.G., Schwabe, J.W.R.

(2020) Nat Commun 11: 3252-3252

Released	2020-07-08
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Homo sapiens
Macromolecule	Deoxynucleotidyltransferase terminal-interacting protein 1 (protein) Histone deacetylase 1 (protein) Mitotic deacetylase-associated SANT domain protein (protein)
Unique Ligands	IHP, K, ZN

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7AO8 \| pdb_00007ao8	Download File View File

Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex

Millard, C.J., Fairall, L., Ragan, T.J., Savva, C.G., Schwabe, J.W.R.

(2020) Nucleic Acids Res 48: 12972-12982

Released	2020-11-11
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 1 (protein) Metastasis-associated protein MTA1 (protein) Methyl-CpG-binding domain protein 2 (protein)
Unique Ligands	IHP, K, ZN

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7AO9 \| pdb_00007ao9	Download File View File

Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex

Millard, C.J., Fairall, L., Ragan, T.J., Savva, C.G., Schwabe, J.W.R.

(2020) Nucleic Acids Res 48: 12972-12982

Released	2020-11-11
Method	ELECTRON MICROSCOPY 6.1 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 1 (protein) Metastasis-associated protein MTA1 (protein) Methyl-CpG-binding domain protein 2 (protein)
Unique Ligands	IHP, K, ZN

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7AOA \| pdb_00007aoa	Download File View File

Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex

Millard, C.J., Fairall, L., Ragan, T.J., Savva, C.G., Schwabe, J.W.R.

(2020) Nucleic Acids Res 48: 12972-12982

Released	2020-11-11
Method	ELECTRON MICROSCOPY 19.4 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 1 (protein) Histone-binding protein RBBP4 (protein) Metastasis-associated protein MTA1 (protein) Methyl-CpG-binding domain protein 2 (protein)
Unique Ligands	IHP, K, ZN

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8VOJ \| pdb_00008voj	Download File View File

The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6

Xie, X., Mao, H., Liau, B., Zheng, N.

To be published

Released	2024-12-04
Method	ELECTRON MICROSCOPY 3.77 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 1 (protein) Isoform 2 of Kelch repeat and BTB domain-containing protein 4 (protein) REST corepressor 1 (protein)
Unique Ligands	A1ACV, IHP, ZN

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8VPQ \| pdb_00008vpq	Download File View File

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML

Xie, X., Liau, B., Zheng, N.

To be published

Released	2024-11-27
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 1 (protein) Isoform 2 of Kelch repeat and BTB domain-containing protein 4 (protein) REST corepressor 1 (protein)
Unique Ligands	IHP, ZN

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8VRT \| pdb_00008vrt	Download File View File

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant

Xie, X., Liau, B., Zheng, N.

To be published

Released	2024-11-27
Method	ELECTRON MICROSCOPY 3.42 Å
Organisms	Homo sapiens
Macromolecule	Histone deacetylase 1 (protein) Kelch repeat and BTB domain-containing protein 4 (protein) REST corepressor 1 (protein)
Unique Ligands	IHP, ZN

1 to 9 of 9 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

5ICN | pdb_00005icn

HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4

6Z2J | pdb_00006z2j

The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

6Z2K | pdb_00006z2k

The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

7AO8 | pdb_00007ao8

Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex

7AO9 | pdb_00007ao9

Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex

7AOA | pdb_00007aoa

Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex

8VOJ | pdb_00008voj

The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6

8VPQ | pdb_00008vpq

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML

8VRT | pdb_00008vrt

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant

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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

5ICN | pdb_00005icn

6Z2J | pdb_00006z2j

6Z2K | pdb_00006z2k

7AO8 | pdb_00007ao8

7AO9 | pdb_00007ao9

7AOA | pdb_00007aoa

8VOJ | pdb_00008voj

8VPQ | pdb_00008vpq

8VRT | pdb_00008vrt