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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "H3F3B"

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Search Summary

This query matches 58 Structures.

Refinements

Structure Determination Methodology

experimental (58)

Scientific Name of Source Organism

	Homo sapiens (58)
	synthetic construct (31)
	Komagataella phaffii GS115 (14)
	Komagataella phaffii (12)
	Komagataella phaffii CBS 7435 (7)
	Mus musculus (4)
	Sus scrofa (3)
	Epstein-barr virus strain ag876 (2)
	Komagataella pastoris (2)
	Human spumaretrovirus (1)

More...

Taxonomy

	Eukaryota (58)
	other sequences (31)
	Duplodnaviria (2)
	Adnaviria (1)
	Riboviria (1)

Experimental Method

	ELECTRON MICROSCOPY (35)
	X-RAY DIFFRACTION (22)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (58)
	DNA (39)
	RNA (29)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (8)
	2.5 - 3.0 (10)
	3.0 - 3.5 (9)
	3.5 - 4.0 (8)
	4.0 - 4.5 (8)
	> 4.5 (11)

Release Date

	2010 - 2014 (9)
	2015 - 2019 (25)
	2020 - 2024 (21)
	2025 - 2029 (3)

Enzyme Classification Name

	Transferases (31)
	Hydrolases (7)
	Oxidoreductases (1)
	Lyases (1)

Symmetry Type

	Asymmetric (51)
	Cyclic (11)

SCOP Classification

	All alpha proteins (15)
	All beta proteins (2)

AllSelected

1 to 25 of 58 Structures

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2L43 \| pdb_00002l43	Download File View File

Structural basis for histone code recognition by BRPF2-PHD1 finger

Qin, S., Zhang, J., Wu, J., Shi, Y.

To be published

Released	2011-08-31
Method	SOLUTION NMR
Organisms	Homo sapiens synthetic construct
Macromolecule	Histone H3.3,LINKER,Bromodomain-containing protein 1 (protein)
Unique Ligands	ZN

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3WTP \| pdb_00003wtp	Download File View File

Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3

Arimura, Y., Shirayama, K., Horikoshi, N., Fujita, R., Kagawa, W., Fukagawa, T., Almouzni, G., Kurumizaka, H.

(2014) Sci Rep 4: 7115-7115

Released	2014-12-03
Method	X-RAY DIFFRACTION 2.67 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 1

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4H9N \| pdb_00004h9n	Download File View File

Complex structure 1 of DAXX/H3.3(sub5)/H4

Elsasser, S.J., Huang, H., Lewis, P.W., Chin, J.W., Allis, D.C., Patel, D.J.

To be published

Released	2012-10-10
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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4H9O \| pdb_00004h9o	Download File View File

Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4

Elsasser, S.J., Huang, H., Lewis, P.W., Chin, J.W., Allis, D.C., Patel, D.J.

To be published

Released	2012-10-10
Method	X-RAY DIFFRACTION 2.053 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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4H9P \| pdb_00004h9p	Download File View File

Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4

Elsasser, S.J., Huang, H., Lewis, P.W., Chin, J.W., Allis, D.C., Patel, D.J.

To be published

Released	2012-10-17
Method	X-RAY DIFFRACTION 2.198 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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4H9Q \| pdb_00004h9q	Download File View File

Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4

Elsasser, S.J., Huang, H., Lewis, P.W., Chin, J.W., Allis, D.C., Patel, D.J.

To be published

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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4H9R \| pdb_00004h9r	Download File View File

Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4

Elsasser, S.J., Huang, H., Lewis, P.W., Chin, J.W., Allis, D.C., Patel, D.J.

To be published

Released	2012-10-17
Method	X-RAY DIFFRACTION 2.197 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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4H9S \| pdb_00004h9s	Download File View File

Complex structure 6 of DAXX/H3.3(sub7)/H4

Elsasser, S.J., Huang, H., Lewis, P.W., Chin, J.W., Allis, D.C., Patel, D.J.

To be published

Released	2012-10-17
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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4HGA \| pdb_00004hga	Download File View File

Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX

Liu, C.P., Xiong, C.Y., Wang, M.Z., Yu, Z.L., Yang, N., Chen, P., Zhang, Z.G., Li, G.H., Xu, R.M.

(2012) Nat Struct Mol Biol 19: 1287-1292

Released	2012-11-07
Method	X-RAY DIFFRACTION 2.799 Å
Organisms	Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PC4

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5B32 \| pdb_00005b32	Download File View File

The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3.

Horikoshi, N., Taguchi, H., Arimura, Y., Kurumizaka, H.

(2016) Open Biol 6:

Released	2016-08-03
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 1
Unique Ligands	CL, MN

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5B33 \| pdb_00005b33	Download File View File

The crystal structure of the H2AZ nucleosome with H3.3.

Horikoshi, N., Taguchi, H., Arimura, Y., Kurumizaka, H.

(2016) Open Biol 6:

Released	2016-08-03
Method	X-RAY DIFFRACTION 2.925 Å
Organisms	Homo sapiens
Macromolecule	Histone H2A.Z (protein) Histone H2B type 1-J (protein) Histone H3.3 (protein) Histone H4 (protein) DNA (146-MER) (nucleic acid)

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5BNV \| pdb_00005bnv	Download File View File

Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer

Huang, H., Patel, D.J.

(2015) Nat Struct Mol Biol 22: 618-626

Released	2015-06-17
Method	X-RAY DIFFRACTION 2.795 Å
Organisms	Homo sapiens
Macromolecule	DNA replication licensing factor MCM2 (protein) Histone H3.3 (protein) Histone H4 (protein)
Unique Ligands	PO4

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5BNX \| pdb_00005bnx	Download File View File

Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer

Huang, H., Patel, D.J.

(2015) Nat Struct Mol Biol 22: 618-626

Released	2015-06-17
Method	X-RAY DIFFRACTION 2.305 Å
Organisms	Homo sapiens
Macromolecule	DNA replication licensing factor MCM2 (protein) Histone H3.3 (protein) Histone H4 (protein) Histone chaperone ASF1B (protein)
Unique Ligands	GOL

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5JA4 \| pdb_00005ja4	Download File View File

Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer

Huang, H., Patel, D.

(2016) Nature 534: 714-718

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.424 Å
Organisms	Homo sapiens
Macromolecule	DNA replication licensing factor MCM2 (protein) Histone H3.3 (protein) Histone H4 (protein) Tonsoku-like protein (protein)
Unique Ligands	GOL, MES

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5KDM \| pdb_00005kdm	Download File View File

Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4

Huang, H., Patel, D.

(2016) Nat Commun 7: 12707-12707

Released	2016-09-07
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Epstein-barr virus strain ag876 Homo sapiens
Macromolecule	Death domain-associated protein 6 (protein) Histone H3.3 (protein) Histone H4 (protein) Major tegument protein (protein)

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5XM0 \| pdb_00005xm0	Download File View File

The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4

Taguchi, H., Horikoshi, N., Kurumizaka, H.

(2018) Nat Commun 9: 1400-1400

Released	2018-03-07
Method	X-RAY DIFFRACTION 2.874 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Histone H2A type 1-B (protein) Histone H2B type 3-A (protein) Histone H3.3 (protein) Histone H4 (protein) DNA (146-MER) (nucleic acid)

Explore in 3D

6A5L \| pdb_00006a5l	Download File View File

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2018-10-03
Method	ELECTRON MICROSCOPY 5.6 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

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6A5O \| pdb_00006a5o	Download File View File

RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2018-10-03
Method	ELECTRON MICROSCOPY 9.9 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

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6A5P \| pdb_00006a5p	Download File View File

RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2018-10-03
Method	ELECTRON MICROSCOPY 7 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

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6A5R \| pdb_00006a5r	Download File View File

RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2018-10-03
Method	ELECTRON MICROSCOPY 8.7 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

Explore in 3D

6A5T \| pdb_00006a5t	Download File View File

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2018-10-03
Method	ELECTRON MICROSCOPY 6.7 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

Explore in 3D

6A5U \| pdb_00006a5u	Download File View File

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2018-10-03
Method	ELECTRON MICROSCOPY 7.6 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

Explore in 3D

6HGT \| pdb_00006hgt	Download File View File

Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation

Maw, J., Le Bihan, Y.V., van Montfort, R.L.M.

To be published

Released	2019-09-04
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Homo sapiens
Macromolecule	Histone H3.3 (protein) Lysine-specific demethylase 4A (protein)
Unique Ligands	OGA, ZN

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6INQ \| pdb_00006inq	Download File View File

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

(2018) Science 362: 595-598

Released	2019-04-03
Method	ELECTRON MICROSCOPY 6.9 Å
Organisms	Homo sapiens Komagataella phaffii GS115 synthetic construct
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

Explore in 3D

6IR9 \| pdb_00006ir9	Download File View File

RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome

Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.

(2019) Science 363: 744-747

Released	2019-02-20
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Homo sapiens Komagataella phaffii CBS 7435 Komagataella phaffii GS115 Linanthus concinnus synthetic construct
Macromolecule	Unique protein chains: 19 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

1 to 25 of 58 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

2L43 | pdb_00002l43

3WTP | pdb_00003wtp

4H9N | pdb_00004h9n

4H9O | pdb_00004h9o

4H9P | pdb_00004h9p

4H9Q | pdb_00004h9q

4H9R | pdb_00004h9r

4H9S | pdb_00004h9s

4HGA | pdb_00004hga

5B32 | pdb_00005b32

5B33 | pdb_00005b33

5BNV | pdb_00005bnv

5BNX | pdb_00005bnx

5JA4 | pdb_00005ja4

5KDM | pdb_00005kdm

5XM0 | pdb_00005xm0

6A5L | pdb_00006a5l

6A5O | pdb_00006a5o

6A5P | pdb_00006a5p

6A5R | pdb_00006a5r

6A5T | pdb_00006a5t

6A5U | pdb_00006a5u

6HGT | pdb_00006hgt

6INQ | pdb_00006inq

6IR9 | pdb_00006ir9