6VEN: Yeast COMPASS
Yeast COMPASS in complex with a ubiquitinated nucleosome. Determined by electron microscopy at 3.37 Å resolution. Released 15 Jan 2020.
- Method
- Electron microscopy
- Resolution
- 3.37 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 18
- Atoms
- 24,028
- Mol. weight
- 475.46 kDa
- Ligands
- ZN, SAM
- Released
- 15 Jan 2020
Explore 6VEN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6VEN contains 67 α-helices and 132 β-strands across 16 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, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 1 |
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| 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 | 2 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-91 | 9 | |
| β-strand | 98 | 1 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-21 | 3 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-121 | 18 | |
Chain E: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 7 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 7 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-36 | 10 | |
| β-strand | 43 | 1 | 8 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| β-strand | 102 | 1 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 57-83 | 27 | |
| β-strand | 89 | 1 | 8 |
| α-helix | 93-101 | 9 | |
| α-helix | 104-122 | 19 | |
8 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 | 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 1.1 | D, H | protein | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| 601 DNA (146-mer) | I | DNA | 146 | synthetic construct | |
| 601 DNA (146-mer) | J | DNA | 146 | synthetic construct | |
| Ubiquitin | K | protein | 80 | Homo sapiens | P0CG48 |
| COMPASS component SWD3 | L | protein | 315 | Saccharomyces cerevisiae | P38123 |
| COMPASS component SWD1 | M | protein | 426 | Saccharomyces cerevisiae | P39706 |
| Histone-lysine N-methyltransferase, H3 lysine-4 specific | N | protein | 358 | Saccharomyces cerevisiae | P38827 |
| COMPASS component BRE2 | O | protein | 505 | Saccharomyces cerevisiae | P43132 |
| COMPASS component SDC1 | P, Q | protein | 175 | Saccharomyces cerevisiae | Q03323 |
1 more molecules are not listed.
Sequence of entity 1 (A, E), FASTA
>6VEN_1 Histone H3.2 (chains A, E)
ARTLQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVALFEDTNLCAIHAKRVTIL
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6VEN_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6VEN_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6VEN_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTS
AK
Sequence of entity 5 (I), FASTA
>6VEN_5 601 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>6VEN_6 601 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 7 (K), FASTA
>6VEN_7 Ubiquitin (chains K)
GSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGC
Sequence of entity 8 (L), FASTA
>6VEN_8 COMPASS component SWD3 (chains L)
MFQFVTPVGTQNGLKATCAKISPDGQFLAITQGLNILIYDINRRTVSQTLVTSHARPFSE
LCWSPDGQCIATASDDFSVEIIHLSYGLLHTFIGHTAPVISLTFNRKGNLLFTSSMDESI
KIWDTLNGSLMKTISAHSEAVVSVDVPMNDSSILSSGSYDGLIRIFDAETGHCLKTLTYD
KDWKRENGVVPISQVKFSENARYLLVKSLDGVVKIWDCIGGCVVRTFQVQPLEKGVLHHS
CGMDFLNPEDGSTPLVISGYENGDIYCWNSDTKSLLQLLDGSLYHHSSPVMSIHCFGNIM
CSLALNGDCCLWRWV
Sequence of entity 9 (M), FASTA
>6VEN_9 COMPASS component SWD1 (chains M)
MNILLQDPFAVLKEHPEKLTHTIENPLRTECLQFSPCGDYLALGCANGALVIYDMDTFRP
ICVPGNMLGAHVRPITSIAWSPDGRLLLTSSRDWSIKLWDLSKPSKPLKEIRFDSPIWGC
QWLDAKRRLCVATIFEESDAYVIDFSNDPVASLLSKSDEKQLSSTPDHGYVLVCTVHTKH
PNIIIVGTSKGWLDFYKFHSLYQTECIHSLKITSSNIKHLIVSQNGERLAINCSDRTIRQ
YEISIDDENSAVELTLEHKYQDVINKLQWNCILFSNNTAEYLVASTHGSSAHELYIWETT
SGTLVRVLEGAEEELIDINWDFYSMSIVSNGFESGNVYVWSVVIPPKWSALAPDFEEVEE
NVDYLEKEDEFDEVDEAEQQQGLEQEEEIAIDLRTREQYDVRGNNLLVERFTIPTDYTRI
IKMQSS
Sequence of entity 10 (N), FASTA
>6VEN_10 Histone-lysine N-methyltransferase, H3 lysine-4 specific (chains N)
MHHHHHHGSSDYKDHDGDYKDHDIDYKDDDDKENLYFQGMDLQNAIKDEEDMLILKQLLS
TYTPTVTPETSAALEYKIWQSRRKVLEEEKASDWQIELNGTLFDSELQPGSSFKAEGFRK
IADKLKINYLPHRRRVHQPLNTVNIHNERNEYTPELCQREESSNKEPSDSVPQEVSSSRD
NRASNRRFQQDIEAQKAAIGTESELLSLNQLNKRKKPVMFARSAIHNWGLYALDSIAAKE
MIIEYVGERIRQPVAEMREKRYLKNGIGSSYLFRVDENTVIDATKKGGIARFINHCCDPN
CTAKIIKVGGRRRIVIYALRDIAASEELTYDYKFEREKDDEERLPCLCGAPNCKGFLN
Sequence of entity 11 (O), FASTA
>6VEN_11 COMPASS component BRE2 (chains O)
MKLGIIPYQEGTDIVYKNALQGQQEGKRPNLPQMEATHQIKSSVQGTSYEFVRTEDIPLN
RRHFVYRPCSANPFFTILGYGCTEYPFDHSGMSVMDRSEGLSISRDGNDLVSVPDQYGWR
TARSDVCIKEGMTYWEVEVIRGGNKKFADGVNNKENADDSVDEVQSGIYEKMHKQVNDTP
HLRFGVCRREASLEAPVGFDVYGYGIRDISLESIHEGKLNCVLENGSPLKEGDKIGFLLS
LPSIHTQIKQAKEFTKRRIFALNSHMDTMNEPWREDAENGPSRKKLKQETTNKEFQRALL
EDIEYNDVVRDQIAIRYKNQLFFEATDYVKTTKPEYYSSDKRERQDYYQLEDSYLAIFQN
GKYLGKAFENLKPLLPPFSELQYNEKFYLGYWQHGEARDESNDKNTTSAKKKKQQQKKKK
GLILRNKYVNNNKLGYYPTISCFNGGTARIISEEDKLEYLDQIRSAYCVDGNSKVNTLDT
LYKEQIAEDIVWDIIDELEQIALQQ
Sequence of entity 12 (P, Q), FASTA
>6VEN_12 COMPASS component SDC1 (chains P, Q)
MNESENSPQHNEVTVPMVEDTSSNADIPMEQIQREDNKNYDKHDNECFDMNGNHNNNSDN
LQFDSVPSSATKDLKNIKSVTNQNVKIEESSSTNSVIEESSEPKISKLENVNLAATVGGS
QTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILKSGEKESNASK
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 for COMPASS recognition of an H2B-ubiquitinated nucleosome. Worden, E.J., Zhang, X., Wolberger, C. Elife (2020) 9. DOI 10.7554/eLife.53199 · 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
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