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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "H3l"

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Search Summary

This query matches 12 Structures.

Refinements

Structure Determination Methodology

experimental (12)

Scientific Name of Source Organism

	Xenopus laevis (11)
	Homo sapiens (6)
	synthetic construct (6)
	Xenopus tropicalis (4)
	Saccharomyces cerevisiae (3)
	Kluyveromyces lactis NRRL Y-1140 (2)
	Saccharomyces cerevisiae S288C (2)
	Vaccinia virus WR (1)

Taxonomy

	Eukaryota (11)
	other sequences (6)
	Varidnaviria (1)

Experimental Method

	ELECTRON MICROSCOPY (9)
	X-RAY DIFFRACTION (3)

Polymer Entity Type

	Protein (12)
	DNA (9)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	3.0 - 3.5 (4)
	3.5 - 4.0 (4)
	> 4.5 (2)

Release Date

	2005 - 2009 (1)
	2015 - 2019 (5)
	2020 - 2024 (6)

Enzyme Classification Name

	Transferases (6)
	Hydrolases (2)

Symmetry Type

	Asymmetric (10)
	Cyclic (3)

SCOP Classification

	All alpha proteins (2)
	Artifacts (1)
	Membrane and cell surface proteins and peptides (1)
	All beta proteins (1)

AllSelected

1 to 12 of 12 Structures

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2HUE \| pdb_00002hue	Download File View File

Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4

English, C.M., Churchill, M.E.A., Tyler, J.K.

(2006) Cell 127: 495-508

Released	2006-11-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Saccharomyces cerevisiae Xenopus laevis
Macromolecule	Anti-silencing protein 1 (protein) Histone H3 (protein) Histone H4 (protein)
Unique Ligands	GOL, SO4, ZN

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5EJ0 \| pdb_00005ej0	Download File View File

The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose

Singh, K., Gittis, A.G., Gitti, R.K., Ostazesky, S.A., Su, H.P., Garboczi, D.N.

(2016) J Virol 90: 5020-5030

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Vaccinia virus WR
Macromolecule	Envelope protein H3 (protein)
Unique Ligands	DHL, EDO, EOH, GOL, MG, MOH, PDO, PG0, POL

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5OY7 \| pdb_00005oy7	Download File View File

Structure of the 4_601_157 tetranucleosome (P1 form)

Ekundayo, B., Richmond, T.J., Schalch, T.

(2017) J Mol Biology 429: 3031-3042

Released	2017-09-20
Method	X-RAY DIFFRACTION 5.774 Å
Organisms	Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	CL

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6G0L \| pdb_00006g0l	Download File View File

Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome

Sundaramoorthy, R., Owen-hughes, T., Norman, D.G., Hughes, A.

(2018) Elife 7:

Released	2018-08-22
Method	ELECTRON MICROSCOPY 10 Å
Organisms	Saccharomyces cerevisiae S288C Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF

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6UGM \| pdb_00006ugm	Download File View File

Structural basis of COMPASS eCM recognition of an unmodified nucleosome

Hsu, P.L., Shi, H., Zheng, N.

(2019) Mol Cell 76: 712

Released	2019-11-20
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Kluyveromyces lactis NRRL Y-1140 Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 12 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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6UH5 \| pdb_00006uh5	Download File View File

Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

Hsu, P.L., Shi, H., Zheng, N.

(2019) Mol Cell 76: 712

Released	2019-11-20
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens Kluyveromyces lactis NRRL Y-1140 Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 13 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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6VZ4 \| pdb_00006vz4	Download File View File

Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state

Leschziner, A.E., Baker, R.W.

(2021) Nat Struct Mol Biol 28: 71-80

Released	2020-12-02
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 8 Unique nucleic acid chains: 2
Unique Ligands	ADP, ATP, BEF, MG

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7CRO \| pdb_00007cro	Download File View File

NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.75 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7CRP \| pdb_00007crp	Download File View File

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7CRQ \| pdb_00007crq	Download File View File

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7CRR \| pdb_00007crr	Download File View File

Native NSD3 bound to 187-bp nucleosome

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.48 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7UNK \| pdb_00007unk	Download File View File

Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex

Bernardes, N.E., Chook, Y.M., Fung, H.Y.J., Chen, Z., Li, Y.

(2022) Proc Natl Acad Sci U S A 119: e2207177119-e2207177119

Released	2022-09-21
Method	ELECTRON MICROSCOPY 3.45 Å
Organisms	Homo sapiens Saccharomyces cerevisiae Xenopus laevis
Macromolecule	Histone H3 (protein) Histone H4 (protein) Histone chaperone (protein) Importin-4 (protein)

1 to 12 of 12 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.

2HUE | pdb_00002hue

Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4

5EJ0 | pdb_00005ej0

The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose

5OY7 | pdb_00005oy7

Structure of the 4_601_157 tetranucleosome (P1 form)

6G0L | pdb_00006g0l

Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome

6UGM | pdb_00006ugm

Structural basis of COMPASS eCM recognition of an unmodified nucleosome

6UH5 | pdb_00006uh5

Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

6VZ4 | pdb_00006vz4

Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state

7CRO | pdb_00007cro

NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP

7CRP | pdb_00007crp

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)

7CRQ | pdb_00007crq

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)

7CRR | pdb_00007crr

Native NSD3 bound to 187-bp nucleosome

7UNK | pdb_00007unk

Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex

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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

2HUE | pdb_00002hue

5EJ0 | pdb_00005ej0

5OY7 | pdb_00005oy7

6G0L | pdb_00006g0l

6UGM | pdb_00006ugm

6UH5 | pdb_00006uh5

6VZ4 | pdb_00006vz4

7CRO | pdb_00007cro

7CRP | pdb_00007crp

7CRQ | pdb_00007crq

7CRR | pdb_00007crr

7UNK | pdb_00007unk