H2B

Histone H2B

• SMART accession number: SM00427
• Description: -
• Interpro abstract (IPR000558):

  Histone H2B is one of the five histones, along with H1/H5, H2A, H3 and H4. Two copies of each of the H2A, H2B, H3, and H4 histones ensemble to form the core of the nucleosome [ (PUBMED:16472024) ]. The nucleosome forms octameric structure that wraps DNA in a left-handed manner. Histones can undergo several different types of post-translational modifications that affect transcription, DNA repair, DNA replication and chromosomal stability.

  The HBR (histone H2B repression) domain within the H2B N terminus is important for nucleosome assembly by histone chaperone FACT [ (PUBMED:27369377) ].

• GO component: nucleosome (GO:0000786)
• GO function: DNA binding (GO:0003677)

There are 5436 H2B domains in 5379 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Luger K, Richmond TJ
• DNA binding within the nucleosome core.
• Curr Opin Struct Biol. 1998; 8: 33-40

The high resolution structure of the nucleosome core particle of chromatin reveals the form of DNA that is predominant in living cells and offers a wealth of information on DNA binding and bending by the histone octamer. Recent studies imply that chromatin is highly dynamic. This propensity for unfolding and refolding stems from the structural design of the nucleosome core. The histone-fold motif, central to nucleosome structure, is also found in other proteins involved in transcriptional regulation.

• Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ
• Crystal structure of the nucleosome core particle at 2.8 A resolution.
• Nature. 1997; 389: 251-60

The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.

• Thatcher TH, Gorovsky MA
• Phylogenetic analysis of the core histones H2A, H2B, H3, and H4.
• Nucleic Acids Res. 1994; 22: 174-9

Despite the ubiquity of histones in eukaryotes and their important role in determining the structure and function of chromatin, no detailed studies of the evolution of the histones have been reported. We have constructed phylogenetic trees for the core histones H2A, H2B, H3, and H4. Histones which form dimers (H2A/H2B and H3/H4) have very similar trees and appear to have co-evolved, with the exception of the divergent sea urchin testis H2Bs, for which no corresponding divergent H2As have been identified. The trees for H2A and H2B also support the theory that animals and fungi have a common ancestor. H3 and H4 are 10-fold less divergent than H2A and H2B. Three evolutionary histories are observed for histone variants. H2A.F/Z-type variants arose once early in evolution, while H2A.X variants arose separately, during the evolution of multicellular animals. H3.3-type variants have arisen in multiple independent events.

Structure (3D structures containing this domain)

3D Structures of H2B domains in PDB

PDB code	Title
1aoi	COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT
1eqz	X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
1f66	2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z
1hio	HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN, ALPHA CARBONS ONLY
1hq3	CRYSTAL STRUCTURE OF THE HISTONE-CORE-OCTAMER IN KCL/PHOSPHATE
1id3	CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS
1kx3	X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
1kx4	X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution
1kx5	X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1m18	LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
1m19	LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
1m1a	LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
1p34	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3a	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3b	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3f	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3g	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3i	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3k	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3l	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3m	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3o	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1p3p	Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants
1s32	Molecular Recognition of the Nucleosomal 'Supergroove'
1tzy	Crystal Structure of the Core-Histone Octamer to 1.90 Angstrom Resolution
1u35	Crystal structure of the nucleosome core particle containing the histone domain of macroH2A
1zbb	Structure of the 4_601_167 Tetranucleosome
1zla	X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core
2aro	Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-Nitrosoglutathione
2cv5	Crystal structure of human nucleosome core particle
2f8n	2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
2fj7	Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element
2hio	HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN
2jss	NMR structure of chaperone Chz1 complexed with histone H2A.Z-H2B
2nqb	Drosophila Nucleosome Structure
2nzd	Nucleosome core particle containing 145 bp of DNA
2pyo	Drosophila nucleosome core
2rvq	2RVQ
2xql	Fitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).
3a6n	The nucleosome containing a testis-specific histone variant, human H3T
3afa	The human nucleosome structure
3an2	The structure of the centromeric nucleosome containing CENP-A
3av1	The human nucleosome structure containing the histone variant H3.2
3av2	The human nucleosome structure containing the histone variant H3.3
3ayw	Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation
3aze	Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation
3azf	Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation
3azg	Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation
3azh	Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation
3azi	Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation
3azj	Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation
3azk	Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation
3azl	Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation
3azm	Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation
3azn	Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation
3b6f	Nucleosome core particle treated with cisplatin
3b6g	Nucleosome core particle treated with oxaliplatin
3c1b	The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure
3c1c	The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure
3c9k	Model of Histone Octamer Tubular Crystals
3kuy	DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent
3kwq	Structural characterization of H3K56Q nucleosomes and nucleosomal arrays
3kxb	Structural characterization of H3K56Q nucleosomes and nucleosomal arrays
3lel	Structural Insight into the Sequence-Dependence of Nucleosome Positioning
3lja	Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome
3lz0	Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1)
3lz1	Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2)
3mgp	Binding of Cobalt ions to the Nucleosome Core Particle
3mgq	Binding of Nickel ions to the Nucleosome Core Particle
3mgr	Binding of Rubidium ions to the Nucleosome Core Particle
3mgs	Binding of Cesium ions to the Nucleosome Core particle
3mnn	A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core
3mvd	Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle
3o62	Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link
3reh	2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145)
3rei	2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride
3rej	2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b)
3rek	2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin
3rel	2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride
3tu4	Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle.
3ut9	Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)
3uta	Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2)
3utb	Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b)
3w96	Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region
3w97	Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region
3w98	Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region
3w99	Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region
3wa9	The nucleosome containing human H2A.Z.1
3waa	The nucleosome containing human H2A.Z.2
3wkj	The nucleosome containing human TSH2B
3wtp	3WTP
3x1s	3X1S
3x1t	3X1T
3x1u	3X1U
3x1v	3X1V
4cay	Crystal structure of a human Anp32e-H2A.Z-H2B complex
4j8u	X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II)
4j8v	X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II)
4j8w	X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II)
4j8x	X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II)
4jjn	Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome
4kgc	Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM
4kha	Structural basis of histone H2A-H2B recognition by the essential chaperone FACT
4kud	Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle
4ld9	Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle
4m6b	Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer
4nft	Crystal structure of human lnkH2B-h2A.Z-Anp32e
4qlc	4QLC
4r8p	4R8P
4wnn	4WNN
4wu8	4WU8
4wu9	4WU9
4x23	4X23
4xuj	4XUJ
4xzq	4XZQ
4ym5	4YM5
4ym6	4YM6
4ys3	4YS3
4z5t	4Z5T
4z66	4Z66
4zux	4ZUX
5av5	5AV5
5av6	5AV6
5av8	5AV8
5av9	5AV9
5avb	5AVB
5avc	5AVC
5ay8	5AY8
5b0y	5B0Y
5b0z	5B0Z
5b24	5B24
5b2i	5B2I
5b2j	5B2J
5b31	5B31
5b32	5B32
5b33	5B33
5b40	5B40
5bt1	5BT1
5chl	5CHL
5cp6	5CP6
5cpi	5CPI
5cpj	5CPJ
5cpk	5CPK
5dnm	5DNM
5dnn	5DNN
5e5a	5E5A
5f99	5F99
5fug	5FUG
5g2e	5G2E
5hq2	5HQ2
5kgf	5KGF

Links (links to other resources describing this domain)

• INTERPRO: IPR000558
• PFAM: histone
• PROSITE: HISTONE_H2B