6KIX: Human MLL1-NCP complex, binding mode1
Cryo-EM structure of human MLL1-NCP complex, binding mode1. Determined by electron microscopy at 4.1 Å resolution. Released 11 Sept 2019.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 14
- Atoms
- 19,900
- Mol. weight
- 379.46 kDa
- Ligands
- SAH, ZN, LYS, GLN
- Released
- 11 Sept 2019
Explore 6KIX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6KIX contains 43 α-helices and 120 β-strands across 12 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.
Chains A and E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 84 | 1 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-41 | 9 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 50-76 | 27 | |
| β-strand | 81 | 1 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101 | 1 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain F: 4 helices, 3 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 | |
| β-strand | 81 | 1 | 6 |
| α-helix | 83-93 | 11 | |
| β-strand | 97 | 1 | 5 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 9 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
Chain K: 4 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3816-3827 | 12 | |
| β-strand | 3834-3835 | 2 | 20 |
| β-strand | 3841-3842 | 2 | 20 |
| β-strand | 3844 | 1 | 21 |
| α-helix | 3849-3850 | 2 | |
| β-strand | 3856-3857 | 2 | 22 |
| β-strand | 3862-3864 | 3 | 23 |
| α-helix | 3867-3878 | 12 | |
| β-strand | 3884-3886 | 3 | 23 |
| β-strand | 3891-3894 | 4 | 23 |
| β-strand | 3898-3899 | 2 | 19 |
| α-helix | 3901-3903 | 3 | |
| β-strand | 3907 | 1 | 24 |
| β-strand | 3915-3916 | 2 | 22 |
| β-strand | 3919-3920 | 2 | 25 |
| β-strand | 3923-3924 | 2 | 25 |
| β-strand | 3927-3928 | 2 | 22 |
| β-strand | 3939 | 1 | 21 |
| β-strand | 3942 | 1 | 24 |
3 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 | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 129 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (145-mer) | I | DNA | 145 | synthetic construct | |
| DNA (145-mer) | J | DNA | 145 | synthetic construct | |
| Retinoblastoma-binding protein 5 | N | protein | 538 | Homo sapiens | Q15291 |
| Histone-lysine N-methyltransferase 2A | K | protein | 216 | Homo sapiens | Q03164 |
| WD repeat-containing protein 5 | R | protein | 334 | Homo sapiens | P61964 |
| Set1/Ash2 histone methyltransferase complex subunit ASH2 | T | protein | 534 | Homo sapiens | Q9UBL3 |
Sequence of entity 1 (A, E), FASTA
>6KIX_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6KIX_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6KIX_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6KIX_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTS
AK
Sequence of entity 5 (I), FASTA
>6KIX_5 DNA (145-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGA
Sequence of entity 6 (J), FASTA
>6KIX_6 DNA (145-MER) (chains J)
TCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 7 (N), FASTA
>6KIX_7 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL
Sequence of entity 8 (K), FASTA
>6KIX_8 Histone-lysine N-methyltransferase 2A (chains K)
NEPPLNPHGSARAEVHLRKSAFDMFNFLASKHRQPPEYNPNDEEEEEVQLKSARRATSMD
LPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREK
YYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRK
IYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN
Sequence of entity 9 (R), FASTA
>6KIX_9 WD repeat-containing protein 5 (chains R)
MATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWL
ASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGK
CLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKL
WDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGH
TDVVISTACHPTENIIASAALENDKTIKLWKSDC
Sequence of entity 10 (T), FASTA
>6KIX_10 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains T)
MDTQAGSVDEENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSG
NTYFLRKQANLKEMCLSALANLTWQSRTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRP
GKMTWPNNIVKTMSKERDVFLVKEHPDPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQS
SAVSTSGNLNGGIAAGSSGKGRGAKRKQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEH
PFNKDGYRYILAEPDPHAPDPEKLELDCWAGKPIPGDLYRACLYERVLLALHDRAPQLKI
SDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYD
KFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTETAKSLPDTYKDKALIKF
KSYLYFEEKDFVDKAEKSLKQTPHSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTV
SINFGPCFKYPPKDLTYRPMSDMGWGAVVEHTLADVLYHVETEVDGRRSPPWEP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
| ZN | Zinc ion | Zn | 1 |
| LYS | Lysine | C6 H15 N2 O2 | 1 |
| GLN | Glutamine | C5 H10 N2 O3 | 1 |
Primary citation
Structural basis of nucleosome recognition and modification by MLL methyltransferases. Xue, H., Yao, T., Cao, M. et al. Nature (2019) 573:445-449. DOI 10.1038/s41586-019-1528-1 · 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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