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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "YNL031C"

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Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Saccharomyces cerevisiae S288C (14)
	synthetic construct (5)
	Aspergillus fumigatus Af293 (3)
	Saccharomyces cerevisiae (3)
	Escherichia coli (2)

Taxonomy

	Eukaryota (16)
	other sequences (5)
	Bacteria (2)

Experimental Method

	ELECTRON MICROSCOPY (10)
	X-RAY DIFFRACTION (6)

Polymer Entity Type

	Protein (16)
	DNA (11)

Refinement Resolution (Å)

	2.0 - 2.5 (1)
	2.5 - 3.0 (2)
	3.0 - 3.5 (3)
	3.5 - 4.0 (6)
	4.0 - 4.5 (3)
	> 4.5 (1)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (2)
	2015 - 2019 (4)
	2020 - 2024 (9)

Enzyme Classification Name

	Hydrolases (5)
	Transferases (3)

Symmetry Type

	Asymmetric (13)
	Cyclic (3)

SCOP Classification

	All alpha proteins (1)
	All beta proteins (2)
	Artifacts (1)

AllSelected

1 to 16 of 16 Structures

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2IDC \| pdb_00002idc	Download File View File

Structure of the Histone H3-Asf1 Chaperone Interaction

Antczak, A.J., Tsubota, T., Kaufman, P.D., Berger, J.M.

(2006) BMC Struct Biol 6: 26-26

Released	2007-01-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	ANTI-SILENCING PROTEIN 1 AND HISTONE H3 CHIMERA (protein)

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4JJN \| pdb_00004jjn	Download File View File

Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome

Wang, F., Li, G., Mohammed, A., Lu, C., Currie, M., Johnson, A., Moazed, D.

(2013) Proc Natl Acad Sci U S A 110: 8495-8500

Released	2013-05-15
Method	X-RAY DIFFRACTION 3.09 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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4KUD \| pdb_00004kud	Download File View File

Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle

Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M.

(2013) Nat Struct Mol Biol 20: 1116-1118

Released	2013-08-07
Method	X-RAY DIFFRACTION 3.203 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 1

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5ZBA \| pdb_00005zba	Download File View File

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

Zhang, L., Serra-Cardona, A., Zhou, H., Wang, M., Yang, N., Zhang, Z., Xu, R.M.

(2018) Cell 174: 818-830.e11

Released	2018-07-25
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Aspergillus fumigatus Af293 Saccharomyces cerevisiae S288C
Macromolecule	DNA damage response protein Rtt109, putative (protein) Histone H3 (protein) Histone H4 (protein) Histone chaperone asf1 (protein)
Unique Ligands	COA, IOD

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5ZBB \| pdb_00005zbb	Download File View File

Crystal structure of Rtt109-Asf1-H3-H4 complex

Zhang, L., Serra-Cardona, A., Zhou, H., Wang, M., Yang, N., Zhang, Z., Xu, R.M.

(2018) Cell 174: 818-830.e11

Released	2018-07-25
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Aspergillus fumigatus Af293 Saccharomyces cerevisiae S288C
Macromolecule	DNA damage response protein Rtt109, putative (protein) Histone H3 (protein) Histone H4 (protein) Histone chaperone asf1 (protein)
Unique Ligands	GOL, IOD, PEG

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6GEJ \| pdb_00006gej	Download File View File

Chromatin remodeller-nucleosome complex at 3.6 A resolution.

Willhoft, O., Chua, E.Y.D., Wilkinson, M., Wigley, D.B.

(2018) Science 362:

Released	2018-10-17
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, ZN

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6GEN \| pdb_00006gen	Download File View File

Chromatin remodeller-nucleosome complex at 4.5 A resolution.

Willhoft, O., Chua, E.Y.D., Wilkinson, M., Wigley, D.B.

(2018) Science 362:

Released	2018-10-17
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, ZN

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7E9C \| pdb_00007e9c	Download File View File

Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome

Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M.

To be published

Released	2022-09-07
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Escherichia coli Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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7E9F \| pdb_00007e9f	Download File View File

Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome

Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M.

To be published

Released	2022-09-07
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Escherichia coli Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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7K7G \| pdb_00007k7g	Download File View File

nucleosome and Gal4 complex

Ruifang, G., Yawen, B.

(2021) Nat Commun 12: 1763-1763

Released	2021-03-31
Method	ELECTRON MICROSCOPY 4.2 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7XAY \| pdb_00007xay	Download File View File

Crystal structure of Hat1-Hat2-Asf1-H3-H4

Yue, Y., Yang, W.S., Xu, R.M.

(2022) Genes Dev 36: 408-413

Released	2022-05-18
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Aspergillus fumigatus Af293 Saccharomyces cerevisiae S288C
Macromolecule	Histone H3 (protein) Histone H4 (protein) Histone acetyltransferase type B subunit 2 (protein) Histone chaperone asf1 (protein) Soluble cytochrome b562,Histone acetyltransferase type B catalytic subunit (protein)
Unique Ligands	COA

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7Z0O \| pdb_00007z0o	Download File View File

Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA

Baudin, F., Murciano, B., Fung, H.K.H., Fromm, S.A., Mueller, C.W.

(2022) Sci Adv 8: eabn5725-eabn5725

Released	2022-04-27
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2

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8GHN \| pdb_00008ghn	Download File View File

Composite model of the yeast Hir Complex with Asf1/H3/H4

Kim, H.J., Murakami, K.

(2024) Mol Cell 84: 2601-2617.e12

Released	2024-07-17
Method	ELECTRON MICROSCOPY 2.96 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 7

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8QKU \| pdb_00008qku	Download File View File

SWR1-nucleosome complex in configuration 1

Jalal, A.S.B., Wigley, D.B.

(2024) Nature 636: 251-257

Released	2024-10-02
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, ZN

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8QKV \| pdb_00008qkv	Download File View File

SWR1-nucleosome complex in configuration 2

Jalal, A.S.B., Wigley, D.B.

(2024) Nature 636: 251-257

Released	2024-10-02
Method	ELECTRON MICROSCOPY 4.7 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, ZN

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9FBW \| pdb_00009fbw	Download File View File

SWR1 lacking Swc5 subunit in complex with hexasome

Jalal, A.S.B., Wigley, D.B.

(2024) Mol Cell 84: 3871

Released	2024-10-02
Method	ELECTRON MICROSCOPY 4.4 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, ZN

1 to 16 of 16 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.

2IDC | pdb_00002idc

Structure of the Histone H3-Asf1 Chaperone Interaction

4JJN | pdb_00004jjn

Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome

4KUD | pdb_00004kud

Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle

5ZBA | pdb_00005zba

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

5ZBB | pdb_00005zbb

Crystal structure of Rtt109-Asf1-H3-H4 complex

6GEJ | pdb_00006gej

Chromatin remodeller-nucleosome complex at 3.6 A resolution.

6GEN | pdb_00006gen

Chromatin remodeller-nucleosome complex at 4.5 A resolution.

7E9C | pdb_00007e9c

Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome

7E9F | pdb_00007e9f

Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome

7K7G | pdb_00007k7g

nucleosome and Gal4 complex

7XAY | pdb_00007xay

Crystal structure of Hat1-Hat2-Asf1-H3-H4

7Z0O | pdb_00007z0o

Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA

8GHN | pdb_00008ghn

Composite model of the yeast Hir Complex with Asf1/H3/H4

8QKU | pdb_00008qku

SWR1-nucleosome complex in configuration 1

8QKV | pdb_00008qkv

SWR1-nucleosome complex in configuration 2

9FBW | pdb_00009fbw

SWR1 lacking Swc5 subunit in complex with hexasome

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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

2IDC | pdb_00002idc

4JJN | pdb_00004jjn

4KUD | pdb_00004kud

5ZBA | pdb_00005zba

5ZBB | pdb_00005zbb

6GEJ | pdb_00006gej

6GEN | pdb_00006gen

7E9C | pdb_00007e9c

7E9F | pdb_00007e9f

7K7G | pdb_00007k7g

7XAY | pdb_00007xay

7Z0O | pdb_00007z0o

8GHN | pdb_00008ghn

8QKU | pdb_00008qku

8QKV | pdb_00008qkv

9FBW | pdb_00009fbw