8CBN: LEDGF/p75 PWWP domain

structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome. Determined by electron microscopy at 3.34 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 3.34 Å
Organisms: Xenopus laevis, synthetic construct, Homo sapiens
Chains: 12
Atoms: 13,669
Mol. weight: 330.52 kDa
Released: 27 Dec 2023

Explore 8CBN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CBN contains 38 α-helices and 30 β-strands across 10 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-74	11
β-strand	83-84	2	2
α-helix	86-113	28
β-strand	118-119	2	1
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	1
α-helix	51-75	25
β-strand	80-81	2	2
α-helix	83-91	9
β-strand	96-98	3	3

Chains C and G: 5 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	80-87	8
α-helix	93-96	4
β-strand	100-102	3	6

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	103-121	19

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-54	8
α-helix	64-74	11
α-helix	75-77	3
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	8
α-helix	84-92	9
β-strand	96-98	3	6

Chains K and L: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10-14	5	11
β-strand	20-24	5	11
β-strand	42-44	3	11
β-strand	49-51	3	11
β-strand	59-60	2	11
α-helix	80-86	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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)
Widom 601 DNA	I	DNA	165	synthetic construct
Widom 601 DNA	J	DNA	165	synthetic construct
PC4 and SFRS1-interacting protein	K, L	protein	530	Homo sapiens	O75475 (AlphaFold model)
Histone H3	A, E	protein	135	Xenopus laevis	P84233

Sequence of entity 1 (B, F), FASTA

>8CBN_1 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 2 (C, G), FASTA

>8CBN_2 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 3 (D, H), FASTA

>8CBN_3 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 4 (I), FASTA

>8CBN_4 WIDOM 601 DNA (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGAC

Sequence of entity 5 (J), FASTA

>8CBN_5 WIDOM 601 DNA (chains J)
GTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAG
TAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAG
AGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Sequence of entity 6 (K, L), FASTA

>8CBN_6 PC4 and SFRS1-interacting protein (chains K, L)
MTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFP
YSENKEKYGKPNKRKGFNEGLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKE
DTDHEEKASNEDVTKAVDITTPKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPKR
GRPAATEVKIPKPRGRPKMVKQPCPSESDIITEEDKSKKKGQEEKQPKKQPKKDEEGQKE
EDKPRKEPDKKEGKKEVESKRKNLAKTGVTSTSDSEEEGDDQEGEKKRKGGRNFQTAHRR
NMLKGQHEKEAADRKRKQEEQMETEQQNKDEGKKPEVKKVEKKRETSMDSRLQRIHAEIK
NSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLY
NKFKNMFLVGEGDSVITQVLNKSLAEQRQHEEANKTKDQGKKGPNKKLEKEQTGSKTLNG
GSDAQDGNQPQHNGESNEDSKDNHEASTKKKPSSEERETEISLKDSTLDN

Sequence of entity 7 (A, E), FASTA

>8CBN_7 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA

Primary citation

Multivalency of nucleosome recognition by LEDGF. Koutna, E., Lux, V., Kouba, T. et al. Nucleic Acids Res (2023) 51:10011-10025. DOI 10.1093/nar/gkad674 · PubMed

Other PDB entries of the same protein (UniProt P62799 (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
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
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
4ZBJ 2.25 Å, UBN1 peptide bound to H3.3/H4/Asf1
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA

Browse structure collections

About this viewer

MolViewer shows 8CBN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.