4DS7: Yeast calmodulin
Crystal structure of yeast calmodulin bound to the C-terminal fragment of spindle pole body protein Spc110. Determined by X-ray diffraction at 2.15 Å resolution. Released 7 Mar 2012.
- Method
- X-ray diffraction
- Resolution
- 2.15 Å
- Organisms
- Kluyveromyces lactis, Saccharomyces cerevisiae S288c
- Chains
- 8
- Atoms
- 5,926
- Mol. weight
- 91.88 kDa
- Ligands
- SR
- Released
- 7 Mar 2012
Explore 4DS7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4DS7 contains 36 α-helices and 16 β-strands across 8 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: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27-29 | 3 | 1 |
| α-helix | 30-39 | 10 | |
| α-helix | 46-56 | 11 | |
| β-strand | 63-65 | 3 | 1 |
| α-helix | 66-78 | 13 | |
| α-helix | 80-93 | 14 | |
| β-strand | 100-101 | 2 | 2 |
| α-helix | 103-112 | 10 | |
| α-helix | 119-129 | 11 | |
| β-strand | 136-137 | 2 | 2 |
| α-helix | 138-144 | 7 | |
Chain B: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27-28 | 2 | 3 |
| α-helix | 30-39 | 10 | |
| α-helix | 46-56 | 11 | |
| β-strand | 64-65 | 2 | 3 |
| α-helix | 66-78 | 13 | |
| α-helix | 80-93 | 14 | |
| β-strand | 101 | 1 | 4 |
| α-helix | 103-112 | 10 | |
| α-helix | 119-127 | 9 | |
| β-strand | 136 | 1 | 4 |
| α-helix | 138-144 | 7 | |
Chain C: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27-29 | 3 | 5 |
| α-helix | 30-39 | 10 | |
| α-helix | 46-56 | 11 | |
| β-strand | 63-65 | 3 | 5 |
| α-helix | 66-78 | 13 | |
| α-helix | 80-93 | 14 | |
| β-strand | 101 | 1 | 6 |
| α-helix | 103-112 | 10 | |
| α-helix | 119-127 | 9 | |
| β-strand | 136 | 1 | 6 |
| α-helix | 138-144 | 7 | |
Chain D: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 28 | 1 | 7 |
| α-helix | 30-39 | 10 | |
| α-helix | 46-56 | 11 | |
| β-strand | 64 | 1 | 7 |
| α-helix | 66-78 | 13 | |
| α-helix | 80-93 | 14 | |
| β-strand | 101 | 1 | 8 |
| α-helix | 103-112 | 10 | |
| α-helix | 119-130 | 12 | |
| β-strand | 136 | 1 | 8 |
| α-helix | 138-144 | 7 | |
Chains E, G and H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 901-933 | 33 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 901-935 | 35 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Calmodulin | A, B, C, D | protein | 147 | Kluyveromyces lactis | O60041 (AlphaFold model) |
| Spindle pole body component 110 | E, F, G, H | protein | 55 | Saccharomyces cerevisiae S288c | P32380 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>4DS7_1 Calmodulin (chains A, B, C, D)
MSQNLTEEQIAEFKEAFALFDKDNSGSISASELATVMRSLGLSPSEAEVADLMNEIDVDG
NHAIEFSEFLALMSRQLKCNDSEQELLEAFKVFDKNGDGLISAAELKHVLTSIGEKLTDA
EVDEMLREVSDGSGEINIKQFAALLSK
Sequence of entity 2 (E, F, G, H), FASTA
>4DS7_2 Spindle pole body component 110 (chains E, F, G, H)
GRGPYFERRLSFKTVALLVLACVRMKRIAFYRRSDDNRLRILRDRIESSSGRISW
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SR | Strontium ion | Sr | 8 |
Water and common crystallization additives (SO4, GOL) are not listed.
Primary citation
The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Viswanath, S., Bonomi, M., Kim, S.J. et al. Mol Biol Cell (2017) 28:3298-3314. DOI 10.1091/mbc.E17-06-0397 · PubMed
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