8OX1: TRF1core
Structure of TRF1core in complex with telomeric nucleosome. Determined by electron microscopy at 2.7 Å resolution. Released 30 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 13,258
- Mol. weight
- 303.14 kDa
- Released
- 30 Aug 2023
Explore 8OX1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OX1 contains 50 α-helices and 20 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-30 | 5 | |
| 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 | 102-120 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
Chain H: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-31 | 7 | |
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
2 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 H3.1 | A, E | protein | 140 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 107 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-C | C, G | protein | 134 | Homo sapiens | Q93077 (AlphaFold model) |
| Histone H2B type 1-C/E/F/G/I | D, H | protein | 130 | Homo sapiens | P62807 (AlphaFold model) |
| Telomeric DNA C strand | I | DNA | 145 | Homo sapiens | |
| Telomeric DNA G strand | J | DNA | 145 | Homo sapiens | |
| Telomeric repeat-binding factor 1 | L | protein | 439 | Homo sapiens | P54274 |
| Telomeric repeat-binding factor 1 | M | protein | 439 | Homo sapiens | P54274 |
Sequence of entity 1 (A, E), FASTA
>8OX1_1 Histone H3.1 (chains A, E)
GPRGMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQ
KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAK
RVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8OX1_2 Histone H4 (chains B, F)
GPRGMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETR
GVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8OX1_3 Histone H2A type 1-C (chains C, G)
GPRGMSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVL
EYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVL
LPKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>8OX1_4 Histone H2B type 1-C/E/F/G/I (chains D, H)
GPRGMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGIS
SKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGT
KAVTKYTSSK
Sequence of entity 5 (I), FASTA
>8OX1_5 Telomeric DNA C strand (chains I)
ATCACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
CTAACCCTAACCCTAACCCTAAGAT
Sequence of entity 6 (J), FASTA
>8OX1_6 Telomeric DNA G strand (chains J)
ATCTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
GGGTTAGGGTTAGGGTTAGGGTGAT
Sequence of entity 7 (L), FASTA
>8OX1_7 Telomeric repeat-binding factor 1 (chains L)
MAEDVSSAAPSPRGCADGRDADPTEEQMAETERNDEEQFECQELLECQVQVGAPEEEEEE
EEDAGLVAEAEAVAAGWMLDFLCLSLCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTACQL
RTIYICQFLTRIAAGKTLDAQFENDERITPLESALMIWGSIEKEHDKLHEEIQNLIKIQA
IAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMIISQKDTFHSFFQHFSYNHMMEKI
KSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETEANLDTRKSVSDK
QSAVTESSEGTVSLLRSHKNLFLSKLQHGTQQQDLNKKERRVGTPQSTKKKKESRRATES
RIPVSKSQPVTPEKHRARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVML
KDRWRTMKKLKLISSDSED
Sequence of entity 8 (M), FASTA
>8OX1_8 Telomeric repeat-binding factor 1 (chains M)
MAEDVSSAAPSPRGCADGRDADPTEEQMAETERNDEEQFECQELLECQVQVGAPEEEEEE
EEDAGLVAEAEAVAAGWMLDFLCLSLCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTACQL
RTIYICQFLTRIAAGKTLDAQFENDERITPLESALMIWGSIEKEHDKLHEEIQNLIKIQA
IAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMIISQKDTFHSFFQHFSYNHMMEKI
KSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETEANLDTRKSVSDK
QSAVTESSEGTVSLLRSHKNLFLSKLQHGTQQQDLNKKERRVGTPQSTKKKKESRRATES
RIPVSKSQPVTPEKHRARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVML
KDRWRTMKKLKLISSDSED
Primary citation
Structural basis of telomeric nucleosome recognition by shelterin factor TRF1. Hu, H., van Roon, A.M., Ghanim, G.E. et al. Sci Adv (2023) 9:eadi4148-eadi4148. DOI 10.1126/sciadv.adi4148 · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
About this viewer
MolViewer shows 8OX1 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.