7UD5: Histone H3

Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome. Determined by electron microscopy at 4.25 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 4.25 Å
Organisms: Xenopus laevis, synthetic construct, Homo sapiens
Chains: 17
Atoms: 22,713
Mol. weight: 414.65 kDa
Ligands: ZN, SAH
Released: 21 Sept 2022

Explore 7UD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UD5 contains 62 α-helices and 123 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-55	11
α-helix	65-78	14
β-strand	83	1	1
α-helix	86-113	28
β-strand	119	1	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	46	1	2
α-helix	51-75	25
β-strand	80	1	1
α-helix	84-93	10
β-strand	97-98	2	3

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	28-35	8
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	78	1	5
α-helix	80-89	10
α-helix	91-96	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	51	1	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	89-98	10
α-helix	102-119	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	6
α-helix	85	1
α-helix	86-113	28
β-strand	119	1	7
α-helix	121-131	11

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	51-75	25
β-strand	80-81	2	6
α-helix	84-93	10

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	8
α-helix	46-72	27
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3

Chain H: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-45	10
α-helix	53-80	28
β-strand	85-86	2	8
α-helix	88-98	11
α-helix	101-120	20

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	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281 (AlphaFold model)
601 DNA (146-mer)	I	DNA	146	synthetic construct
601 DNA (146-mer)	J	DNA	146	synthetic construct
cDNA FLJ56846, highly similar to Zinc finger protein HRX	K	protein	226	Homo sapiens	B4DIJ7
WD repeat-containing protein 5	L	protein	335	Homo sapiens	P61964
Set1/Ash2 histone methyltransferase complex subunit ASH2	M	protein	534	Homo sapiens	Q9UBL3
Retinoblastoma-binding protein 5	N	protein	538	Homo sapiens	Q15291
Polyubiquitin-B	O	protein	81	Homo sapiens	P0CG47
Protein dpy-30 homolog	P, Q	protein	104	Homo sapiens	Q9C005

Sequence of entity 1 (A, E), FASTA

>7UD5_1 Histone H3 (chains A, E)
MARTLQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVALFEDTNLCAIHAKRVTI
LPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>7UD5_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>7UD5_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>7UD5_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYT
SAK

Sequence of entity 5 (I), FASTA

>7UD5_5 601 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>7UD5_6 601 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 7 (K), FASTA

>7UD5_7 cDNA FLJ56846, highly similar to Zinc finger protein HRX (chains K)
MFRFHKPEEANEPPLNPHGSARAEVHLRKSAFDMFNFLASKHRQPPEYNPNDEEEEEVQL
KSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVI
RSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQ
KHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN

Sequence of entity 8 (L), FASTA

>7UD5_8 WD repeat-containing protein 5 (chains L)
GSATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEW
LASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSG
KCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHF
NRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLK
LWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQG
HTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Sequence of entity 9 (M), FASTA

>7UD5_9 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains M)
MDTQAGSVDEENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSG
NTYFLRKQANLKEMCLSALANLTWQSRTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRP
GKMTWPNNIVKTMSKERDVFLVKEHPDPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQS
SAVSTSGNLNGGIAAGSSGKGRGAKRKQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEH
PFNKDGYRYILAEPDPHAPDPEKLELDCWAGKPIPGDLYRACLYERVLLALHDRAPQLKI
SDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYD
KFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTETAKSLPDTYKDKALIKF
KSYLYFEEKDFVDKAEKSLKQTPHSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTV
SINFGPCFKYPPKDLTYRPMSDMGWGAVVEHTLADVLYHVETEVDGRRSPPWEP

Sequence of entity 10 (N), FASTA

>7UD5_10 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL

Sequence of entity 11 (O), FASTA

>7UD5_11 Polyubiquitin-B (chains O)
QGSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGC

Sequence of entity 12 (P, Q), FASTA

>7UD5_12 Protein dpy-30 homolog (chains P, Q)
GAMDPMEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRA
YLDQTVVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Primary citation

Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Rahman, S., Hoffmann, N.A., Worden, E.J. et al. Proc Natl Acad Sci U S A (2022) 119:e2205691119-e2205691119. DOI 10.1073/pnas.2205691119 · 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

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