9GD3: Histone H3.2

Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Determined by electron microscopy at 3.0 Å resolution. Released 18 Sept 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae S288C
Chains: 12
Atoms: 19,030
Mol. weight: 589.36 kDa
Ligands: BEF, ADP, MG
Released: 18 Sept 2024

Explore 9GD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GD3 contains 91 α-helices and 43 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-56	11
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-114	29
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-119	19

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-56	11
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	97-98	2	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	107-110	4

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-120	20

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281 (AlphaFold model)
DNA (231-mer)	I	DNA	231	synthetic construct
DNA (231-mer)	J	DNA	231	synthetic construct
Chromo domain-containing protein 1	T, W	protein	1468	Saccharomyces cerevisiae S288C	P32657

Sequence of entity 1 (A, E), FASTA

>9GD3_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9GD3_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9GD3_3 Histone H2A type 1 (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9GD3_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 5 (I), FASTA

>9GD3_5 DNA (231-MER) (chains I)
CTTATGTGATGGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAA
TTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTA
ACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCA
TGTATTGAACAGCGACCTTGCCGGTGCCAGTCGGATAGTGTTCCGAGCTCC

Sequence of entity 6 (J), FASTA

>9GD3_6 DNA (231-MER) (chains J)
GGAGCTCGGAACACTATCCGACTGGCACCGGCAAGGTCGCTGTTCAATACATGCACAGGA
TGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCG
GGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGC
CTCGGCACCGGGATTCTCCAGGGCGGCCGCGTATAGGGTCCATCACATAAG

Sequence of entity 7 (T, W), FASTA

>9GD3_7 Chromo domain-containing protein 1 (chains T, W)
MAAKDISTEVLQNPELYGLRRSHRAAAHQQNYFNDSDDEDDEDNIKQSRRKRMTTIEDDE
DEFEDEEGEEDSGEDEDEEDFEEDDDYYGSPIKQNRSKPKSRTKSKSKSKPKSQSEKQST
VKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGID
IVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLK
RLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLED
GTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPR
FEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIF
ARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGK
KTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLI
TGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKK
DVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASN
HPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQM
VRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINL
MTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILE
YAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAED
HVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQ
LEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYK
AILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEK
HATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDL
KYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRD
DPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYL
LSFLRGGLNTKSPSADIGSKKLPTGPSKKRQRKPANHSKSMTPEITSSEPANGPPSKRMK
ALPKGPAALINNTRLSPNSPTPPLKSKVSRDNGTRQSSNPSSGSAHEKEYDSMDEEDCRH
TMSAIRTSLKRLRRGGKSLDRKEWAKILKTELTTIGNHIESQKGSSRKASPEKYRKHLWS
YSANFWPADVKSTKLMAMYDKITESQKK

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT. Engeholm, M., Roske, J.J., Oberbeckmann, E. et al. Mol Cell (2024) 84:3423. DOI 10.1016/j.molcel.2024.08.022 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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