6J2P: Saccharomyces cerevisiae Spp1
Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3. Determined by X-ray diffraction at 2.85 Å resolution. Released 11 Sept 2019.
- Method
- X-ray diffraction
- Resolution
- 2.85 Å
- Organism
- Saccharomyces cerevisiae S288c
- Chains
- 8
- Atoms
- 3,183
- Mol. weight
- 61.05 kDa
- Ligands
- ZN
- Released
- 11 Sept 2019
Explore 6J2P in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6J2P contains 20 α-helices and 35 β-strands across 7 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, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 1 |
| β-strand | 29 | 1 | 1 |
| β-strand | 36-38 | 3 | 2 |
| β-strand | 45-47 | 3 | 2 |
| α-helix | 48-51 | 4 | |
| α-helix | 55-57 | 3 | |
| β-strand | 61-63 | 3 | 3 |
| α-helix | 67-70 | 4 | |
| β-strand | 88-89 | 2 | 3 |
| β-strand | 92 | 1 | 4 |
| β-strand | 101 | 1 | 4 |
| α-helix | 102 | 1 | |
| α-helix | 111-113 | 3 | |
Chain B: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 5 |
| β-strand | 29 | 1 | 5 |
| β-strand | 36-38 | 3 | 6 |
| β-strand | 45-47 | 3 | 6 |
| α-helix | 49-51 | 3 | |
| α-helix | 55-57 | 3 | |
| β-strand | 61-63 | 3 | 7 |
| β-strand | 88-89 | 2 | 7 |
| α-helix | 90-91 | 2 | |
| β-strand | 92 | 1 | 8 |
| α-helix | 93 | 1 | |
| α-helix | 100 | 1 | |
| β-strand | 101 | 1 | 8 |
| α-helix | 102-103 | 2 | |
| α-helix | 111-114 | 4 | |
Chain C: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 9 |
| β-strand | 29 | 1 | 9 |
| β-strand | 36-38 | 3 | 10 |
| β-strand | 45-47 | 3 | 10 |
| α-helix | 55-60 | 6 | |
| β-strand | 61-63 | 3 | 11 |
| α-helix | 67-71 | 5 | |
| β-strand | 88-89 | 2 | 11 |
| α-helix | 90-91 | 2 | |
| β-strand | 92 | 1 | 12 |
| α-helix | 93 | 1 | |
| β-strand | 101 | 1 | 12 |
Chain D: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 13 |
| β-strand | 29 | 1 | 13 |
| β-strand | 36-38 | 3 | 14 |
| β-strand | 45-47 | 3 | 14 |
| α-helix | 55-57 | 3 | |
| β-strand | 61-63 | 3 | 15 |
| α-helix | 67-70 | 4 | |
| β-strand | 88-89 | 2 | 15 |
| α-helix | 90-91 | 2 | |
| β-strand | 92 | 1 | 16 |
| α-helix | 93 | 1 | |
| β-strand | 101 | 1 | 16 |
Chains E, F and G: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 2 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| COMPASS component SPP1 | A, B, C, D | protein | 123 | Saccharomyces cerevisiae S288c | Q03012 (AlphaFold model) |
| Histone H3 | E, F, G, H | protein | 7 | Saccharomyces cerevisiae S288c | P61830 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>6J2P_1 COMPASS component SPP1 (chains A, B, C, D)
SHNMSLPQWCPPHSTLKRNPTTGEDVYCICKRPDYGELMVGCDGCDDWFHFTCLHIPEQF
KDLVFSFYCPYCQAGITGKNKNGEGSLPKTLWKRKCRISDCYKPCLQDSKYCSEEHGREF
VND
Sequence of entity 2 (E, F, G, H), FASTA
>6J2P_2 Histone H3 (chains E, F, G, H)
ARTKQTA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 12 |
Primary citation
Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1. He, C., Liu, N., Xie, D. et al. Biochem J (2019) 476:1957-1973. DOI 10.1042/BCJ20190091 · PubMed
Other PDB entries of the same protein (UniProt Q03012 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6VEN 3.37 Å, Yeast COMPASS in complex with a ubiquitinated nucleosome
- 6BX3 4.3 Å, Structure of histone H3k4 methyltransferase
Browse structure collections
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