6UH5: COMPASS eCM recognition of the H2Bub nucleosome

Structural basis of COMPASS eCM recognition of the H2Bub nucleosome. Determined by electron microscopy at 3.5 Å resolution. Released 20 Nov 2019.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Xenopus laevis, synthetic construct, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Chains: 19
Atoms: 24,466
Mol. weight: 438.12 kDa
Ligands: SAM, ZN
Released: 20 Nov 2019

Explore 6UH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UH5 contains 81 α-helices and 137 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
α-helix	40-42	3
α-helix	47-54	8
α-helix	65-74	10
α-helix	75-77	3
β-strand	83-84	2	1
α-helix	87-113	27
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
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: 7 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	47-72	26
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	92-96	5
α-helix	100	1
β-strand	101	1	6
α-helix	102	1

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	54-76	23
β-strand	85-86	2	4
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	45-56	12
α-helix	65-78	14
β-strand	83	1	7
α-helix	90-113	24
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 5 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	50-52	3
α-helix	54-76	23
β-strand	80	1	7
α-helix	83-92	10
β-strand	97	1	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-33	6
β-strand	42-43	2	9
α-helix	47-71	25
β-strand	78	1	10
α-helix	80-88	9
β-strand	101-102	2	3
α-helix	113-115	3

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	51	1	10
α-helix	53-55	3
α-helix	57-80	24
β-strand	85-86	2	9
α-helix	90-98	9
α-helix	102-120	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	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	H	protein	125	Xenopus laevis	P02281 (AlphaFold model)
DNA (146-mer)	I	DNA	146	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
Ubiquitin	Q	protein	76	Homo sapiens	P0CG47
H3 N-terminus	R	protein	8	Xenopus laevis	P84233

3 more molecules are not listed.

Sequence of entity 1 (A, E), FASTA

>6UH5_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCGIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6UH5_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6UH5_3 Histone H2A (chains C, G)
AKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK

Sequence of entity 4 (D), FASTA

>6UH5_4 Histone H2B (chains D)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 5 (H), FASTA

>6UH5_5 Histone H2B (chains H)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTC
YTSAK

Sequence of entity 6 (I), FASTA

>6UH5_6 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (J), FASTA

>6UH5_7 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 8 (K), FASTA

>6UH5_8 Swd3 (chains K)
MCDLDSVSDLTLTLRMLQFDKQVLPASGKISTSCQISPDGELIAICQNTDMLVYEISSSK
MMKLTTTHKECINCLCWSPDSKCIASGSEDFTVEITHIIYGRIRRLMGHTAPVISICYNN
KGNILCSSSMDESIKEWHVLSGTALKTMSAHSDAVVSIDIPKFDSSILSSGSYDGLIRIF
DTESGHCLKTLTYDKDWIAEDGVVPISTVKFSRNGKFLLVKSLDNVVKLWEYTRGTVVRT
FLWPHQETKAKLKYNCGLELIYPQGKDPLVISGNDSGSMCVWNVYSKNLVQKIDEKHRNS
PLISISASYDKVATLSLNGECNLFRVH

Sequence of entity 9 (M), FASTA

>6UH5_9 Histone-lysine N-methyltransferase, H3 lysine-4 specific (chains M)
YQQIEQNGIIRDNQIALNEKEFDSTLASTTGSFIAEGFKKIPDKLKSSYLLHHRRLAQPL
NTVHNHQEQNFMALNGTESTNQEADLEQDNHNASSRLNRVFQRRFQQDIEAQRAAIGFES
DLLSLNQLTKRKKPVTFARSAIHNWGLYALEPIAAKEMIIEYVGESIRQPVAEMREKRYI
KSGIGSSYLFRIDENTVIDATKRGGIARFINHCCEPSCTAKIIKVDGRKRIVIYALRDIG
TNEELTYDYKFERETDEGERLPCLCGAPSCKGFLN

Sequence of entity 10 (N), FASTA

>6UH5_10 Swd1 (chains N)
MANLLLQDPFGVLKEYPEKLTHTLEVPVAAVCVKFSPRGDYLAVGCSNGAIIIYDMDSLK
PIAMLGTHSGAHTRSVQSVCWSNDGRYLWSSGRDWYAKLWDMTQPTKCFQQYKFDGPLWS
CHVVRWNVCIVTVVEEPTAYVLTLTDRQNAFHCFPLLEQDQDISGHGYTLVACPHPTIES
IIITGTSKGWINAFQLDLESGFEDKIRCCYEEKIANANIKQIIISPSGTRIAINGSDRTI
RQYQLIVEDNESEGGSSHSVSIELEHKYQDIINRLQWNTIFFSNHSGEYLVASAHGSSAH
DLYLWETSSGSLVRVLEGADEELLDIDWNFYSMRIASNGFESGWVYMWSIVIPPKWSALA
PDFEEVEENIDYQEKENEFDIMDDDNNLQAMTEAEEIAIDLCTPEKYDVRGNDISMPSFV
IPIDYEGVIIQQHWAHQEQ

Sequence of entity 11 (Q), FASTA

>6UH5_11 Ubiquitin (chains Q)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 12 (R), FASTA

>6UH5_12 H3 N-terminus (chains R)
ARTMQTAR

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	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

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