7TN2: Histone H3

Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps. Determined by electron microscopy at 2.3 Å resolution. Released 2 Mar 2022.

Method: Electron microscopy
Resolution: 2.3 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae
Chains: 11
Atoms: 19,507
Mol. weight: 380.98 kDa
Released: 2 Mar 2022

Explore 7TN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TN2 contains 82 α-helices and 45 β-strands across 9 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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	40	1
β-strand	41	1	1
α-helix	42	1
α-helix	46-54	9
α-helix	64-75	12
β-strand	83-84	2	2
α-helix	86-113	28
β-strand	118-119	2	3
α-helix	121-130	10

Chains B and 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	3
α-helix	50-75	26
β-strand	80-81	2	2
α-helix	83-91	9
β-strand	96-98	3	4

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	5
α-helix	47-72	26
β-strand	77-78	2	6
α-helix	80-89	10
α-helix	93-96	4
β-strand	100-102	3	7
α-helix	113-115	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	6
α-helix	53-80	28
β-strand	85-86	2	5
α-helix	88-98	11
α-helix	102-119	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	118-119	2	9
α-helix	121-131	11

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	10
α-helix	47-72	26
β-strand	77-78	2	11
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	4

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	11
α-helix	53-80	28
β-strand	85-86	2	10
α-helix	88-98	11
α-helix	101-119	19

Chain W: 44 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	132-134	3
α-helix	144-146	3
β-strand	147	1	1
β-strand	179-186	8	12
α-helix	204-208	5
β-strand	212-217	6	12
β-strand	226-228	3	12
α-helix	230-233	4
α-helix	239-246	8
α-helix	247-252	6
α-helix	253-258	6
α-helix	264-282	19
β-strand	287-295	9	13
β-strand	305-311	7	13
β-strand	320-323	4	13
α-helix	324-330	7
α-helix	332-342	11
α-helix	348-350	3
α-helix	378-393	16
β-strand	398-399	2	14
α-helix	401-402	2
α-helix	407-420	14
β-strand	428-432	5	14
α-helix	434-436	3
α-helix	437-446	10
β-strand	453-455	3	14
α-helix	460-470	11
α-helix	480-481	2
β-strand	487-491	5	14
α-helix	492-497	6
α-helix	499-503	5
β-strand	507-513	7	14
α-helix	515-518	4
α-helix	524-530	7
β-strand	534-540	7	14
α-helix	550-559	10
α-helix	577-589	13
α-helix	591-593	3
β-strand	595	1	14
β-strand	609-616	8	15
α-helix	620-630	11
α-helix	634-638	5
α-helix	651-660	10
α-helix	662-664	3
α-helix	668-674	7
α-helix	686-692	7
α-helix	695-709	15
β-strand	714-718	5	15
α-helix	721-734	14
β-strand	738-741	4	15
α-helix	747-757	11
β-strand	766-770	5	15
β-strand	785-788	4	15
α-helix	795-802	8
β-strand	814-821	8	15
α-helix	826-843	18
α-helix	1012-1022	11
α-helix	1029-1031	3
α-helix	1032-1037	6
α-helix	1046-1071	26
β-strand	1119	1	16
β-strand	1122	1	17
β-strand	1125	1	17
β-strand	1129	1	16
α-helix	1130-1147	18
α-helix	1177-1190	14
α-helix	1195-1199	5
α-helix	1250-1265	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	122	Xenopus laevis	P02281 (AlphaFold model)
DNA Tracking Strand	I	DNA	226	synthetic construct
DNA Lagging Strand	J	DNA	226	synthetic construct
Chromo domain-containing protein 1	W	protein	1159	Saccharomyces cerevisiae	P32657

Sequence of entity 1 (A, E), FASTA

>7TN2_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>7TN2_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>7TN2_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>7TN2_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISCKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>7TN2_5 DNA Tracking Strand (chains I)
AGTTCATCCCTTATGTGATGGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAG
GCCGCTCAATTGGTCGTAGACAGCTCTAGCAACCGCTTAAACGCACGTACGCGCTGTCCC
CCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATAC
ATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAGTCGGAT

Sequence of entity 6 (J), FASTA

>7TN2_6 DNA Lagging Strand (chains J)
ATCCGACTGGCACCGGCAAGGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACA
CGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTAC
GTGCGTTTAAGCGGTTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGAT
TCTCCAGGGCGGCCGCGTATAGGGTCCATCACATAAGGGATGAACT

Sequence of entity 7 (W), FASTA

>7TN2_7 Chromo domain-containing protein 1 (chains W)
GPQSTVKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPED
FHGIDIVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQ
VRGLKRLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQR
ASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYT
SQRPRFEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFI
SWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNP
RAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVA
NRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFIL
RRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNEL
KKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVL
IFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGG
LGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARK
KMILEYAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVL
NHAEDHVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEE
YVKEQLEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEV
RALYKAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEIL
EKLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLS
RVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSW
TQIRDDPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGR
RVDYLLSFLRGGLNTKSPS

Primary citation

Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Nodelman, I.M., Das, S., Faustino, A.M. et al. Nat Struct Mol Biol (2022) 29:121-129. DOI 10.1038/s41594-021-00719-x · 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

Browse structure collections

About this viewer

MolViewer shows 7TN2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.