8OW0: Histone H4
Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome. Determined by electron microscopy at 3.4 Å resolution. Released 9 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 25
- Atoms
- 37,971
- Mol. weight
- 787.73 kDa
- Released
- 9 Aug 2023
Explore 8OW0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OW0 contains 190 α-helices and 89 β-strands across 23 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.
Chains a and e: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 134-147 | 14 | |
| α-helix | 155-169 | 15 | |
| β-strand | 177-178 | 2 | 1 |
| α-helix | 180-207 | 28 | |
| α-helix | 215-225 | 11 | |
Chain A: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 230-247 | 18 | |
| α-helix | 256-317 | 62 | |
Chain b: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-41 | 10 | |
| α-helix | 49-77 | 29 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-93 | 10 | |
| β-strand | 98 | 1 | 2 |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 219-246 | 28 | |
| α-helix | 256-323 | 68 | |
Chain c: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-38 | 10 | |
| β-strand | 44-45 | 2 | 4 |
| α-helix | 48-75 | 28 | |
| β-strand | 79-80 | 2 | 3 |
| α-helix | 82-91 | 10 | |
| α-helix | 95-98 | 4 | |
| β-strand | 103-104 | 2 | 6 |
Chain d: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-39 | 4 | |
| α-helix | 42-52 | 11 | |
| β-strand | 57-58 | 2 | 3 |
| α-helix | 60-88 | 29 | |
| β-strand | 92-93 | 2 | 4 |
| α-helix | 95-105 | 11 | |
| α-helix | 108-126 | 19 | |
Chain f: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-42 | 11 | |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 5 |
| α-helix | 84-94 | 11 | |
| β-strand | 98-99 | 2 | 6 |
| β-strand | 100 | 1 | 7 |
| β-strand | 102 | 1 | 7 |
Chain g: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 29-38 | 10 | |
| β-strand | 44-45 | 2 | 8 |
| α-helix | 48-75 | 28 | |
| β-strand | 79-80 | 2 | 9 |
| α-helix | 82-91 | 10 | |
| α-helix | 93-98 | 6 | |
| β-strand | 103 | 1 | 2 |
| α-helix | 110-112 | 3 | |
14 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 |
|---|
| C0N3 DNA | D | DNA | 153 | Saccharomyces cerevisiae | |
| C0N3 DNA | E | DNA | 153 | Saccharomyces cerevisiae | |
| Histone H4 | b, f | protein | 103 | Saccharomyces cerevisiae | P02309 (AlphaFold model) |
| Histone H2B.1 | d, h | protein | 131 | Saccharomyces cerevisiae | P02293 (AlphaFold model) |
| Histone H3-like centromeric protein CSE4 | a, e | protein | 229 | Saccharomyces cerevisiae | P36012 (AlphaFold model) |
| Histone H2A.1 | c, g | protein | 132 | Saccharomyces cerevisiae | P04911 (AlphaFold model) |
| Centromere-binding protein 1 | A, B | protein | 351 | Saccharomyces cerevisiae | P17106 |
| Inner kinetochore subunit MCM16 | H | protein | 181 | Saccharomyces cerevisiae | Q12262 |
| Inner kinetochore subunit CTF3 | I | protein | 733 | Saccharomyces cerevisiae | Q12748 |
| Inner kinetochore subunit MCM22 | K | protein | 239 | Saccharomyces cerevisiae | P47167 |
| Inner kinetochore subunit IML3 | L | protein | 245 | Saccharomyces cerevisiae | P38265 |
| Inner kinetochore subunit CHL4 | N | protein | 458 | Saccharomyces cerevisiae | P38907 |
8 more molecules are not listed.
Sequence of entity 1 (D), FASTA
>8OW0_1 C0N3 DNA (chains D)
ATAAGTCACATGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAATATTAGTGTATTTGATTTCCGAAAGTTAAA
AAAGAAATAGTAAGAAATATATATTTCATTGAA
Sequence of entity 2 (E), FASTA
>8OW0_2 C0N3 DNA (chains E)
TTCAATGAAATATATATTTCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTA
ATATTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGA
CCAATTGAGCGGCCTCGGCACCATGTGACTTAT
Sequence of entity 3 (b, f), FASTA
>8OW0_3 Histone H4 (chains b, f)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 4 (d, h), FASTA
>8OW0_4 Histone H2B.1 (chains d, h)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (a, e), FASTA
>8OW0_5 Histone H3-like centromeric protein CSE4 (chains a, e)
MSSKQQWVSSAIQSDSSGRSLSNVNRLAGDQQSINDRALSLLQRTRATKNLFPRREERRR
YESSKSDLDIETDYEDQAGNLEIETENEEEAEMETEVPAPVRTHSYALDRYVRQKRREKQ
RKQSLKRVEKKYTPSELALYEIRKYQRSTDLLISKIPFARLVKEVTDEFTTKDQDLRWQS
MAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRGQFI
Sequence of entity 6 (c, g), FASTA
>8OW0_6 Histone H2A.1 (chains c, g)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 7 (A, B), FASTA
>8OW0_7 Centromere-binding protein 1 (chains A, B)
MNSLANNNKLSTEDEEIHSARKRGYNEEQNYSEARKKQRDQGLLSQESNDGNIDSALLSE
GATLKGTQSQYESGLTSNKDEKGSDDEDASVAEAAVAATVNYTDLIQGQEDSSDAHTSNQ
TNANGEHKDSLNGERAITPSNEGVKPNTSLEGMTSSPMESTQQSKNDMLIPLAEHDRGPE
HQQDDEDNDDADIDLKKDISMQPGRRGRKPTTLATTDEWKKQRKDSHKEVERRRRENINT
AINVLSDLLPVRESSKAAILACAAEYIQKLKETDEANIEKWTLQKLLSEQNASQLASANE
KLQEELGNAYKEIEYMKRVLRKEGIEYEDMHTHKKQENERKSTRSDNPHEA
Sequence of entity 8 (H), FASTA
>8OW0_8 Inner kinetochore subunit MCM16 (chains H)
MTNSSEKQWERIQQLEKEHVEVYRELLITLDRLYLIRKHNHAVILSHTQQRLLEIRHQLQ
INLEKTALLIRLLEKPDNTNVLFTKLQNLLEESNSLDYELLQSLGAQSSLHKQLIESRAE
RDELMSKLIELSSKFPKPTIPPDDSDTAGKQVEVEKENETIQELMIALQIHSGYTNISYT
I
Sequence of entity 9 (I), FASTA
>8OW0_9 Inner kinetochore subunit CTF3 (chains I)
MSLILDDIILSLTNANERTPPQALKTTLSLLYEKSKQYGLSSPQLQALVRLLCETSIIDT
VTKVYIVENCFLPDGYLTKELLLEIINHLGTPTVFSRYRIQTPPVLQSALCKWLVHVYFL
FPVHSEREHNISSSIWLHLWQFSFLQKWITPLVIWQATTPVDVKPWKLSIIKRCAMHPGY
RDAPGSATLILQRFQCLVGASSQITESIITINCNRKTLKSHRNLKLDAHFLSILKRILSR
AHPANFPADTVQNTIDMYLSEIHQLGADSIYPLRLQSLPEYVPSDSTVSLWDVTSLEQLA
QNWPQLHIPNDVDYMMKPSLNSNVLLPRKVMSRDSLKHLYSSIILIKNSRDESSSPYEWC
IWQLKRCFAHQIETPQEVIPIIISVSSMDNKLSSRIIQTFCNLKYLKLDELTLKKVCGGI
LPLWKPELISGTREFFVKFMASIFMWSTRDGHDNNCTFSETCFYVLQMITNWVLDDKLIA
LGLTLLHDMQSLLTLDKIFNNATSNRFSTMAFISSLDILTQLSKQTKSDYAIQYLIVGPD
IMNKVFSSDDPLLLSAACRYLVATKNKLMQYPSTNKFVRMQNQYIMDLTNYLYRNKVLSS
KSLFGVSPDFFKQILENLYIPTADFKNAKFFTITGIPALSYICIIILRRLETAENTKIKF
TSGIINEETFNNFFRVHHDEIGQHGWIKGVNNIHDLRVKILMHLSNTANPYRDIAAFLFT
YLKSLSKYSVQNS
Sequence of entity 10 (K), FASTA
>8OW0_10 Inner kinetochore subunit MCM22 (chains K)
MDVEKDVLDVYIKNLENQIGNKRYFLKQAQGAIDEITKRSLDTEGKPVNSEVFTELLRKP
MFFSERADPIGFSLTSNFLSLRAQSSSEWLSLMNDQSVDQKAMLLLQNNINSDLKELLRK
LQHQMTIMDSKKQDHAHIRTRKARNKELWDSLADFLKGYLVPNLDDNDESIDSLTNEVML
LMKRLIEHDLNLTLNDFSSKTIPIYRLLLRANIITVIEGSTNPGTKYIKLIDFNETSLT
Sequence of entity 11 (L), FASTA
>8OW0_11 Inner kinetochore subunit IML3 (chains L)
MPYTWKFLGISKQLSLENGIAKLNQLLNLEVDLDIQTIRVPSDPDGGTAADEYIRYEMRL
DISNLDEGTYSKFIFLGNSKMEVPMFLCYCGTDNRNEVVLQWLKAEYGVIMWPIKFEQKT
MIKLADASIVHVTKENIEQITWFSSKLYFEPETQDKNLRQFSIEIPRESCEGLALGYGNT
MHPYNDAIVPYIYNETGMAVERLPLTSVILAGHTKIMRESIVTSTRSLRNRVLAVVLQSI
QFTSE
Sequence of entity 12 (N), FASTA
>8OW0_12 Inner kinetochore subunit CHL4 (chains N)
MSNELRLEDNYVPTSDTLVVFKQLMKLPVTVLYDLTLSWFAKFGGSFDGDIYLLTETLDL
LIEKGVRRNVIVNRILYVYWPDGLNVFQLAEIDCHLMISKPEKFKWLPSKALRGDGKPYV
VKLQPAKFIENLQTDLAKIYHCHVYMFKHPSLPVLITRIQLFDSNNLFLSTPNIGSINKE
SLYNKLDKFQGKPLISRRPYYVAFPLNSPIIFHSVDKDIYARLVLQSISRTISERETIIF
KPVQKIPVKSIHNIMTLLGPSRFAESMGPWECYASANFERSPLHDYKKHQGLTGKKVMVR
EFDDSFLNDDENFYGKEEPEIRRLRLEKNMIKFKGSANGVMDQKYNDLKEFNEHVHNIRN
GKKNEDSGEPVYISRYSSLVPIEKVGFTLKNEINSRIITIKLKFNGNDIFGGLHELCDKN
LINIDKVPGWLAGENGSFSGTIMNGDFQREQVAKGGLL
Primary citation
Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. Dendooven, T., Zhang, Z., Yang, J. et al. Sci Adv (2023) 9:eadg7480-eadg7480. DOI 10.1126/sciadv.adg7480 · 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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