6R25: Lysine-specific histone demethylase 1B
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3. Determined by electron microscopy at 4.61 Å resolution. Released 24 Apr 2019.
- Method
- Electron microscopy
- Resolution
- 4.61 Å
- Organisms
- Homo sapiens, Xenopus laevis, synthetic construct
- Chains
- 13
- Atoms
- 18,654
- Mol. weight
- 304.54 kDa
- Ligands
- ZN, FAD
- Released
- 24 Apr 2019
Explore 6R25 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6R25 contains 82 α-helices and 64 β-strands across 11 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 | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 84 | 1 | 16 |
| α-helix | 86-112 | 27 | |
| β-strand | 118-119 | 2 | 17 |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 17 |
| α-helix | 50-75 | 26 | |
| β-strand | 81 | 1 | 16 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 18 |
Chain C: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 19 |
| α-helix | 47-71 | 25 | |
| β-strand | 78 | 1 | 20 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 21 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 51 | 1 | 20 |
| α-helix | 53-78 | 26 | |
| β-strand | 85-86 | 2 | 19 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 22 |
| α-helix | 86-112 | 27 | |
| β-strand | 118-119 | 2 | 23 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 23 |
| α-helix | 50-74 | 25 | |
| β-strand | 80-81 | 2 | 22 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-97 | 2 | 21 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 24 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 25 |
| α-helix | 80-87 | 8 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 18 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 25 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 24 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
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 |
|---|
| Lysine-specific histone demethylase 1B | K | protein | 776 | Homo sapiens | Q8NB78 (AlphaFold model) |
| Npac | L | protein | 12 | Homo sapiens | Q49A26 (AlphaFold model) |
| Histone H3 | M | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H3 | A, E | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 129 | Xenopus laevis | P06897 |
| H2B | D, H | protein | 126 | Xenopus laevis | P02281 |
| DNA (147-mer) | I | DNA | 147 | synthetic construct | |
| DNA (147-mer) | J | DNA | 147 | synthetic construct | |
Sequence of entity 1 (K), FASTA
>6R25_1 Lysine-specific histone demethylase 1B (chains K)
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDG
YDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKT
YRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPD
CVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRP
DVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCV
QEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGI
KVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCD
LIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGI
QFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKL
AEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEK
KMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKH
SVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMA
YSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Sequence of entity 2 (L), FASTA
>6R25_2 NPAC (chains L)
DPHFHHFLLSQT
Sequence of entity 3 (M), FASTA
>6R25_3 Histone H3 (chains M)
ARTMQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 4 (A, E), FASTA
>6R25_4 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 5 (B, F), FASTA
>6R25_5 H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 6 (C, G), FASTA
>6R25_6 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 7 (D, H), FASTA
>6R25_7 H2B (chains D, H)
MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 8 (I), FASTA
>6R25_8 DNA (147-MER) (chains I)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 9 (J), FASTA
>6R25_9 DNA (147-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| FAD | Flavin-adenine dinucleotide | C27 H33 N9 O15 P2 | 1 |
Primary citation
A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Marabelli, C., Marrocco, B., Pilotto, S. et al. Cell Rep (2019) 27:387-399.e7. DOI 10.1016/j.celrep.2019.03.061 · PubMed
Other PDB entries of the same protein (UniProt Q8NB78 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
- 4GUT 2.0 Å, Crystal structure of LSD2-NPAC
- 7XE2 2.05 Å, Crystal structure of LSD2 in complex with trans-4-Br-PCPA
- 7XE1 2.07 Å, Crystal structure of LSD2 in complex with cis-4-Br-PCPA
- 4FWE 2.13 Å, Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A
- 4GUS 2.23 Å, Crystal structure of LSD2-NPAC with H3 in space group P3221
- 4GUU 2.3 Å, Crystal structure of LSD2-NPAC with tranylcypromine
- 4GUR 2.51 Å, Crystal structure of LSD2-NPAC with H3 in space group P21
- 4FWF 2.7 Å, Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic
- 7XE3 2.82 Å, Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)
- 4FWJ 2.9 Å, Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A
- 4GU1 2.94 Å, Crystal structure of LSD2
Browse structure collections
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