6G0L: Histone H3
Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome. Determined by electron microscopy at 10.0 Å resolution. Released 22 Aug 2018.
- Method
- Electron microscopy
- Resolution
- 10.0 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae S288C
- Chains
- 12
- Atoms
- 27,526
- Mol. weight
- 556.72 kDa
- Ligands
- ADP, BEF
- Released
- 22 Aug 2018
Explore 6G0L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6G0L contains 110 α-helices and 69 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: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 47-56 | 10 | |
| α-helix | 64-78 | 15 | |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 2 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 27-36 | 10 | |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 3 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 4 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 3 |
| α-helix | 55-78 | 24 | |
| α-helix | 88-98 | 11 | |
| α-helix | 101-120 | 20 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-56 | 8 | |
| α-helix | 66-78 | 13 | |
| β-strand | 83-84 | 2 | 5 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 6 |
| α-helix | 123-131 | 9 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 6 |
| α-helix | 48-75 | 28 | |
| β-strand | 80-81 | 2 | 5 |
| α-helix | 82 | 1 | |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 4 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-33 | 7 | |
| β-strand | 43 | 1 | 7 |
| α-helix | 47-72 | 26 | |
| α-helix | 80-89 | 10 | |
| α-helix | 91-97 | 7 | |
| β-strand | 101-102 | 2 | 2 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 86 | 1 | 7 |
| α-helix | 90-98 | 9 | |
| 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 | A, E | protein | 136 | Xenopus laevis | Q92133 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | A0A1L8G0S8 (AlphaFold model) |
| Histone H2A type 1 | C | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H4 | D, H | protein | 126 | Xenopus laevis | P02281 (AlphaFold model) |
| Histone H2A type 1 | G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| DNA (176-mer) | I | DNA | 176 | synthetic construct | |
| DNA (177-mer) | J | DNA | 177 | synthetic construct | |
| Chromo domain-containing protein 1 | M, W | protein | 1468 | Saccharomyces cerevisiae S288C | P32657 |
Sequence of entity 1 (A, E), FASTA
>6G0L_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCGIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6G0L_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C), FASTA
>6G0L_3 Histone H2A type 1 (chains C)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGRVLPNIQSVLLPKK
TESAKSAKSK
Sequence of entity 4 (D, H), FASTA
>6G0L_4 Histone H4 (chains D, H)
MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (G), FASTA
>6G0L_5 Histone H2A type 1 (chains G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESAKSAKSK
Sequence of entity 6 (I), FASTA
>6G0L_6 DNA (176-MER) (chains I)
ATACGCGGCCGCCCATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTC
TAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTAC
TCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGATTAACGATGCTGGGCATA
Sequence of entity 7 (J), FASTA
>6G0L_7 DNA (177-MER) (chains J)
TATGCCCAGCATCGTTAATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAA
TCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGC
TGTCTACGACCAATTGAGCGGCCTTCGGCACCGGGATTCTGATGGGCGGCCGCGTAT
Sequence of entity 8 (M, W), FASTA
>6G0L_8 Chromo domain-containing protein 1 (chains M, 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 |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
| BEF | Beryllium trifluoride ion | Be F3 | 2 |
Primary citation
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. Sundaramoorthy, R., Hughes, A.L., El-Mkami, H. et al. Elife (2018) 7. DOI 10.7554/eLife.35720 · PubMed
Other PDB entries of the same protein (UniProt Q92133 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3MEA 1.26 Å, Crystal structure of the SGF29 in complex with H3K4me3
- 3MEU 1.28 Å, Crystal structure of SGF29 in complex with H3R2me2sK4me3
- 3ME9 1.37 Å, Crystal structure of SGF29 in complex with H3K4me3 peptide
- 3H91 1.5 Å, Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide
- 3O7A 1.67 Å, Crystal structure of PHF13 in complex with H3K4me3
- 3MEV 1.83 Å, Crystal structure of SGF29 in complex with R2AK4me3
- 3GL6 1.9 Å, Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide
- 4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
- 3MET 2.0 Å, Crystal structure of SGF29 in complex with H3K4me2
- 7CRQ 3.15 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
- 7CRP 3.2 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)
- 7UNK 3.45 Å, Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex
Browse structure collections
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