Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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H3 Histone H3

SMART accession number:	SM00428
Description:	-
Interpro abstract (IPR000164):	This entry includes histone H3 and its variant, CENP-A (Cse4 in budding yeast, Cnp1 in fission yeast, and CID/CenH3 in fruit flies). Two primate-specific forms of H3, known as H3.X and H3.Y, are found in the brain [ (PUBMED:20819935) ]. Histone H3 is one of the five histones, along with H1/H5, H2A, H2B 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. H3 is a highly conserved protein of 135 amino acid residues [ (PUBMED:8121801) (PUBMED:2041803) ]. Histones can undergo several different types of post-translational modifications that affect transcription, DNA repair, DNA replication and chromosomal stability. Eukaryotic centromeres consists of an unique nucleosome in which CENP-A can be found [ (PUBMED:22729156) ]. Human CENP-A nucleosome forms a histone octamer containing two each of histones H2A, H2B, H4 and CENP-A. Similar to the H3-containing nucleosome, the CENP-A nucleosome wraps DNA in a left-handed orientation [ (PUBMED:21743476) (PUBMED:22127263) ]. CENP-A nucleosomes function as a scaffold on which other kinetochore proteins assemble. CENP-A may serves as an epigenetic marker for kinetochore assembly [ (PUBMED:24666101) ]. Deposition of CENP-A to the centromere requires histone chaperone HJURP (Holliday junction recognition protein) [ (PUBMED:21478274) ].
GO component:	nucleosome (GO:0000786)
GO function:	DNA binding (GO:0003677)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 9119 H3 domains in 8899 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing H3 domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with H3 domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing H3 domain in the selected taxonomic class.

• 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
  • Display abstract

  • 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
  • Display abstract

  • 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
  • Display abstract

  • 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 H3 domains in PDB

  PDB code	Main view	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
  2hue		Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
  2io5		Crystal structure of the CIA- histone H3-H4 complex
  2l5a		Structural basis for recognition of centromere specific histone H3 variant by nonhistone Scm3
  2ly8		The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the centromere-specific Cse4/H4 histone variant
  2nqb		Drosophila Nucleosome Structure
  2nzd		Nucleosome core particle containing 145 bp of DNA
  2pyo		Drosophila nucleosome core
  2yfv		The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4
  2yfw		Heterotetramer structure of Kluyveromyces lactis Cse4,H4
  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
  3nqj		Crystal structure of (CENP-A/H4)2 heterotetramer
  3nqu		Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer
  3o62		Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link
  3r45		Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP
  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
  4eo5		Yeast Asf1 bound to H3/H4G94P mutant
  4h9n		Complex structure 1 of DAXX/H3.3(sub5)/H4
  4h9o		Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4
  4h9p		Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4
  4h9q		Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4
  4h9r		Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4
  4h9s		Complex structure 6 of DAXX/H3.3(sub7)/H4
  4hga		Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX
  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
  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
  4qlc		4QLC
  4r8p		4R8P
  4uuz		4UUZ
  4wu8		4WU8
  4wu9		4WU9
  4x23		4X23
  4xuj		4XUJ
  4xzq		4XZQ
  4ym5		4YM5
  4ym6		4YM6
  4ys3		4YS3
  4z2m		4Z2M
  4z5t		4Z5T
  4z66		4Z66
  4zbj		4ZBJ
  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
  5bnv		5BNV
  5bnx		5BNX
  5bo0		5BO0
  5bs7		5BS7
  5bsa		5BSA
  5c3i		5C3I
  5cp6		5CP6
  5cpi		5CPI
  5cpj		5CPJ
  5cpk		5CPK
  5dnm		5DNM
  5dnn		5DNN
  5e5a		5E5A
  5f99		5F99
  5hq2		5HQ2
  5ja4		5JA4
  5kdm		5KDM
  5kgf		5KGF

• Links (links to other resources describing this domain)

• PROSITE	HISTONE_H3_2
  PFAM	histone
  INTERPRO	IPR000164

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