7K78: Antibody and nucleosome complex
antibody and nucleosome complex. Determined by electron microscopy at 3.1 Å resolution. Released 31 Mar 2021.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organisms
- Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Mus musculus
- Chains
- 12
- Atoms
- 14,125
- Mol. weight
- 252.92 kDa
- Released
- 31 Mar 2021
Explore 7K78 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7K78 contains 41 α-helices and 65 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 | 135-147 | 13 | |
| α-helix | 155-167 | 13 | |
| β-strand | 177-178 | 2 | 1 |
| α-helix | 180-207 | 28 | |
| β-strand | 212-213 | 2 | 2 |
| α-helix | 215-225 | 11 | |
Chains B and F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-93 | 10 | |
| β-strand | 97-99 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-37 | 9 | |
| β-strand | 44-45 | 2 | 4 |
| α-helix | 48-74 | 27 | |
| β-strand | 79-80 | 2 | 5 |
| α-helix | 82-90 | 9 | |
| α-helix | 93-98 | 6 | |
| β-strand | 102-104 | 3 | 6 |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-52 | 11 | |
| β-strand | 57-58 | 2 | 5 |
| α-helix | 60-87 | 28 | |
| β-strand | 92-93 | 2 | 4 |
| α-helix | 95-105 | 11 | |
| α-helix | 109-128 | 20 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 134-147 | 14 | |
| α-helix | 155-167 | 13 | |
| β-strand | 177-178 | 2 | 7 |
| α-helix | 180-207 | 28 | |
| β-strand | 212-213 | 2 | 8 |
| α-helix | 215-224 | 10 | |
Chain G: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-37 | 9 | |
| β-strand | 44-45 | 2 | 9 |
| α-helix | 49-74 | 26 | |
| β-strand | 79-80 | 2 | 10 |
| α-helix | 82-90 | 9 | |
| β-strand | 102-104 | 3 | 3 |
Chain K: 4 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25-27 | 3 | 11 |
| β-strand | 32-34 | 3 | 12 |
| β-strand | 40-47 | 8 | 11 |
| α-helix | 51-53 | 3 | |
| β-strand | 54-62 | 9 | 12 |
| β-strand | 66-74 | 9 | 12 |
| β-strand | 79-82 | 4 | 12 |
| β-strand | 87 | 1 | 11 |
| β-strand | 90-95 | 6 | 11 |
| β-strand | 100-105 | 6 | 11 |
| α-helix | 110-112 | 3 | |
| β-strand | 114-122 | 9 | 12 |
| β-strand | 129-132 | 4 | 12 |
| β-strand | 136-140 | 5 | 12 |
| α-helix | 160-161 | 2 | |
| β-strand | 162-164 | 3 | 13 |
| β-strand | 168-170 | 3 | 14 |
| β-strand | 177-187 | 11 | 13 |
| β-strand | 191-196 | 6 | 14 |
| β-strand | 203-207 | 5 | 14 |
| β-strand | 211-212 | 2 | 14 |
| α-helix | 213 | 1 | |
| β-strand | 220-233 | 14 | 13 |
| β-strand | 243-248 | 6 | 14 |
| β-strand | 255-256 | 2 | 14 |
| β-strand | 261-263 | 3 | 14 |
Chain L: 4 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25-28 | 4 | 15 |
| β-strand | 32-34 | 3 | 16 |
| β-strand | 40-47 | 8 | 15 |
| α-helix | 51-53 | 3 | |
| β-strand | 54-62 | 9 | 16 |
| β-strand | 66-74 | 9 | 16 |
| β-strand | 79-82 | 4 | 16 |
| α-helix | 84-86 | 3 | |
| β-strand | 87 | 1 | 15 |
| β-strand | 90-95 | 6 | 15 |
| β-strand | 100-105 | 6 | 15 |
| α-helix | 110-112 | 3 | |
| β-strand | 114-122 | 9 | 16 |
| β-strand | 129-132 | 4 | 16 |
| β-strand | 136-140 | 5 | 16 |
| β-strand | 162-164 | 3 | 17 |
| β-strand | 168-171 | 4 | 18 |
| β-strand | 177-183 | 7 | 17 |
| β-strand | 191-196 | 6 | 18 |
| β-strand | 203-207 | 5 | 18 |
| β-strand | 211-212 | 2 | 18 |
| α-helix | 213 | 1 | |
| β-strand | 220-225 | 6 | 17 |
| β-strand | 228-233 | 6 | 17 |
| β-strand | 242-248 | 7 | 18 |
| β-strand | 255-256 | 2 | 18 |
| β-strand | 261-264 | 4 | 18 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cse4 | A, E | protein | 139 | Saccharomyces cerevisiae | |
| Histone H4 | B, F | protein | 103 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02309 (AlphaFold model) |
| Histone H2A.1 | C, G | protein | 132 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04911 (AlphaFold model) |
| Histone H2B.1 | D, H | protein | 131 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02293 (AlphaFold model) |
| DNA (136-mer) | I | DNA | 136 | Saccharomyces cerevisiae | |
| DNA (136-mer) | J | DNA | 136 | Saccharomyces cerevisiae | |
| scFv | K, L | protein | 265 | Mus musculus | |
Sequence of entity 1 (A, E), FASTA
>7K78_1 Cse4 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPKKYTPSELALYEIRKYQRSTD
LLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKR
ITIMKKDMQLARRIRGQFI
Sequence of entity 2 (B, F), FASTA
>7K78_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7K78_3 Histone H2A.1 (chains C, G)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 4 (D, H), FASTA
>7K78_4 Histone H2B.1 (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>7K78_5 DNA (136-MER) (chains I)
TCGGGTCACATGATGATATTTGATTTTATTATATTTTTAAAAAAAGTAAAAAATAAAAAG
TAGTTTATTTTTAAAAAATAAAATTTAAAATATTAGTGTATTTGATTTCCGAAAGTTAAA
AAAGAAATAGTAAGCT
Sequence of entity 6 (J), FASTA
>7K78_6 DNA (136-MER) (chains J)
AGCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTAATATTTTAAATTTTATT
TTTTAAAAATAAACTACTTTTTATTTTTTACTTTTTTTAAAAATATAATAAAATCAAATA
TCATCATGTGACCCGA
Sequence of entity 7 (K, L), FASTA
>7K78_7 scFv (chains K, L)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA
Primary citation
Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation. Guan, R., Lian, T., Zhou, B.R. et al. Nat Commun (2021) 12:1763-1763. DOI 10.1038/s41467-021-21985-9 · PubMed
Other PDB entries of the same protein (UniProt P02309 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6RXK 1.35 Å, Crystal structure of CobB wt in complex with H4K16-Butyryl peptide
- 1Q1A 1.5 Å, Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP…
- 1SZD 1.5 Å, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent…
- 6RXJ 1.6 Å, Crystal structure of CobB wt in complex with H4K16-Acetyl peptide
- 4TWJ 1.65 Å, The structure of Sir2Af2 bound to a myristoylated histone peptide
- 6RXQ 1.7 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr…
- 6RXR 1.7 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr…
- 1SZC 1.75 Å, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent…
- 4TWI 1.79 Å, The structure of Sir2Af1 bound to a succinylated histone peptide
- 6RXP 1.8 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide
- 1E6I 1.87 Å, Bromodomain from GCN5 complexed with acetylated H4 peptide
- 6RXM 1.92 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide
Browse structure collections
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