6UGM: Histone H3
Structural basis of COMPASS eCM recognition of an unmodified nucleosome. Determined by electron microscopy at 3.7 Å resolution. Released 20 Nov 2019.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organisms
- Xenopus laevis, synthetic construct, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
- Chains
- 18
- Atoms
- 23,609
- Mol. weight
- 429.24 kDa
- Ligands
- ZN, SAM
- Released
- 20 Nov 2019
Explore 6UGM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6UGM contains 75 α-helices and 118 β-strands across 15 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 | 40-42 | 3 | |
| α-helix | 47-54 | 8 | |
| α-helix | 65-75 | 11 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 87-112 | 26 | |
| α-helix | 121-130 | 10 | |
Chain B: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| α-helix | 50-53 | 4 | |
| α-helix | 55-74 | 20 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 84-93 | 10 | |
| β-strand | 98 | 1 | 2 |
Chain C: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-32 | 6 | |
| α-helix | 47-71 | 25 | |
| α-helix | 78-79 | 2 | |
| α-helix | 80-87 | 8 | |
| β-strand | 101-102 | 2 | 3 |
Chain D: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 54-80 | 27 | |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 64-74 | 11 | |
| β-strand | 83-84 | 2 | 4 |
| α-helix | 97-113 | 17 | |
| β-strand | 118-119 | 2 | 5 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 5 |
| α-helix | 54-76 | 23 | |
| β-strand | 80-81 | 2 | 4 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain G: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-32 | 6 | |
| α-helix | 47-71 | 25 | |
| β-strand | 78 | 1 | 6 |
| α-helix | 79 | 1 | |
| α-helix | 80-87 | 8 | |
| α-helix | 91-96 | 6 | |
| β-strand | 102 | 1 | 2 |
Chain H: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 51 | 1 | 6 |
| α-helix | 54-73 | 20 | |
| α-helix | 77-80 | 4 | |
| α-helix | 90-98 | 9 | |
| α-helix | 101-103 | 3 | |
| α-helix | 104-120 | 17 | |
7 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 | 135 | Xenopus laevis | Q92133 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 107 | Xenopus laevis | Q6AZJ8 (AlphaFold model) |
| Histone H2B | D | protein | 125 | Xenopus laevis | P02281 (AlphaFold model) |
| Histone H2B 1.1 | H | protein | 125 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (146-mer) | I | DNA | 147 | synthetic construct | |
| DNA (146-mer) | J | DNA | 146 | synthetic construct | |
| Swd3 | K | protein | 327 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CLY5 |
| Histone-lysine N-methyltransferase, H3 lysine-4 specific | M | protein | 275 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CIT4 |
| Swd1 | N | protein | 439 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CXF3 |
| H3 N-terminus | R | protein | 3 | Xenopus laevis | |
| Spp1 | X | protein | 342 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CRQ4 |
2 more molecules are not listed.
Sequence of entity 1 (A, E), FASTA
>6UGM_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCGIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6UGM_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6UGM_3 Histone H2A (chains C, G)
AKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK
Sequence of entity 4 (D), FASTA
>6UGM_4 Histone H2B (chains D)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK
Sequence of entity 5 (H), FASTA
>6UGM_5 Histone H2B 1.1 (chains H)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK
Sequence of entity 6 (I), FASTA
>6UGM_6 DNA (146-MER) (chains I)
CTCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 7 (J), FASTA
>6UGM_7 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 8 (K), FASTA
>6UGM_8 Swd3 (chains K)
MCDLDSVSDLTLTLRMLQFDKQVLPASGKISTSCQISPDGELIAICQNTDMLVYEISSSK
MMKLTTTHKECINCLCWSPDSKCIASGSEDFTVEITHIIYGRIRRLMGHTAPVISICYNN
KGNILCSSSMDESIKEWHVLSGTALKTMSAHSDAVVSIDIPKFDSSILSSGSYDGLIRIF
DTESGHCLKTLTYDKDWIAEDGVVPISTVKFSRNGKFLLVKSLDNVVKLWEYTRGTVVRT
FLWPHQETKAKLKYNCGLELIYPQGKDPLVISGNDSGSMCVWNVYSKNLVQKIDEKHRNS
PLISISASYDKVATLSLNGECNLFRVH
Sequence of entity 9 (M), FASTA
>6UGM_9 Histone-lysine N-methyltransferase, H3 lysine-4 specific (chains M)
YQQIEQNGIIRDNQIALNEKEFDSTLASTTGSFIAEGFKKIPDKLKSSYLLHHRRLAQPL
NTVHNHQEQNFMALNGTESTNQEADLEQDNHNASSRLNRVFQRRFQQDIEAQRAAIGFES
DLLSLNQLTKRKKPVTFARSAIHNWGLYALEPIAAKEMIIEYVGESIRQPVAEMREKRYI
KSGIGSSYLFRIDENTVIDATKRGGIARFINHCCEPSCTAKIIKVDGRKRIVIYALRDIG
TNEELTYDYKFERETDEGERLPCLCGAPSCKGFLN
Sequence of entity 10 (N), FASTA
>6UGM_10 Swd1 (chains N)
MANLLLQDPFGVLKEYPEKLTHTLEVPVAAVCVKFSPRGDYLAVGCSNGAIIIYDMDSLK
PIAMLGTHSGAHTRSVQSVCWSNDGRYLWSSGRDWYAKLWDMTQPTKCFQQYKFDGPLWS
CHVVRWNVCIVTVVEEPTAYVLTLTDRQNAFHCFPLLEQDQDISGHGYTLVACPHPTIES
IIITGTSKGWINAFQLDLESGFEDKIRCCYEEKIANANIKQIIISPSGTRIAINGSDRTI
RQYQLIVEDNESEGGSSHSVSIELEHKYQDIINRLQWNTIFFSNHSGEYLVASAHGSSAH
DLYLWETSSGSLVRVLEGADEELLDIDWNFYSMRIASNGFESGWVYMWSIVIPPKWSALA
PDFEEVEENIDYQEKENEFDIMDDDNNLQAMTEAEEIAIDLCTPEKYDVRGNDISMPSFV
IPIDYEGVIIQQHWAHQEQ
Sequence of entity 11 (R), FASTA
>6UGM_11 H3 N-terminus (chains R)
TMQ
Sequence of entity 12 (X), FASTA
>6UGM_12 Spp1 (chains X)
MSLPSWCPRYDSRKHDPKTGEEVYCICKKPDTGELMVGCDGCDDWFHFSCLKIPEKYRDL
VFSFYCSYCSAGITGPALINGGKLPKTLWKRKCRLPECYTECDANSRSKYCSKKHAVQYV
QSIVDKLNLPGVDKIALLRQLLNETTSLEEFKTLGRDKLPEVTSPLSKDQYSKLLENDQH
LNKLINEHDELVSVKLSKLNEEDAVIEKYVNWIGEVNERLSPHFNQPTGRKKSKSASKVT
ICGYHNEFTIPRSVEEFLDKLLQLKEDENSNITSVDGVCVKTKCAKHQDWITLSQNDLSE
QKDSLENVKRRLDLLISVRTNQLRISFFEQEMSNRVLPGVKT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| SAM | S-adenosylmethionine | C15 H22 N6 O5 S | 1 |
Primary citation
Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS. Hsu, P.L., Shi, H., Leonen, C. et al. Mol Cell (2019) 76:712. DOI 10.1016/j.molcel.2019.10.013 · 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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