8OVW: CBF1-CCAN bound topologically to centromeric DNA
Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA. Determined by electron microscopy at 3.4 Å resolution. Released 9 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 17
- Atoms
- 28,461
- Mol. weight
- 654.58 kDa
- Released
- 9 Aug 2023
Explore 8OVW in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OVW contains 161 α-helices and 71 β-strands across 15 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: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 230-248 | 19 | |
| α-helix | 256-319 | 64 | |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 219-247 | 29 | |
| α-helix | 256-323 | 68 | |
Chain H: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-38 | 34 | |
| α-helix | 47-73 | 27 | |
| α-helix | 81-93 | 13 | |
| α-helix | 97-132 | 36 | |
| α-helix | 136-138 | 3 | |
| α-helix | 149-171 | 23 | |
Chain I: 44 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-12 | 10 | |
| α-helix | 26-37 | 12 | |
| β-strand | 40 | 1 | 1 |
| α-helix | 42-54 | 13 | |
| α-helix | 60-69 | 10 | |
| β-strand | 73 | 1 | 1 |
| α-helix | 76-78 | 3 | |
| α-helix | 79-88 | 10 | |
| β-strand | 93 | 1 | 2 |
| β-strand | 96 | 1 | 2 |
| α-helix | 100-103 | 4 | |
| α-helix | 104-116 | 13 | |
| α-helix | 131-138 | 8 | |
| α-helix | 146-156 | 11 | |
| α-helix | 165-175 | 11 | |
| α-helix | 183-198 | 16 | |
| α-helix | 205-210 | 6 | |
| α-helix | 217-221 | 5 | |
| α-helix | 228-240 | 13 | |
| α-helix | 248-263 | 16 | |
| α-helix | 264-266 | 3 | |
| β-strand | 288-289 | 2 | 3 |
| α-helix | 296-301 | 6 | |
| β-strand | 306-307 | 2 | 3 |
| α-helix | 312-316 | 5 | |
| α-helix | 333-336 | 4 | |
| α-helix | 340-347 | 8 | |
| α-helix | 349-350 | 2 | |
| α-helix | 355-368 | 14 | |
| α-helix | 379-386 | 8 | |
| α-helix | 390-400 | 11 | |
| α-helix | 403-408 | 6 | |
| α-helix | 410-420 | 11 | |
| α-helix | 421-423 | 3 | |
| α-helix | 432-449 | 18 | |
| α-helix | 457-474 | 18 | |
| α-helix | 479-493 | 15 | |
| α-helix | 506-523 | 18 | |
| α-helix | 532-534 | 3 | |
| α-helix | 539-547 | 9 | |
| α-helix | 551-568 | 18 | |
| α-helix | 578-589 | 12 | |
| α-helix | 590-594 | 5 | |
| β-strand | 603 | 1 | 4 |
| β-strand | 606 | 1 | 4 |
| α-helix | 608-615 | 8 | |
| α-helix | 640-653 | 14 | |
| α-helix | 667-676 | 10 | |
| α-helix | 678-683 | 6 | |
| α-helix | 693-704 | 12 | |
| α-helix | 712-720 | 9 | |
| α-helix | 726-728 | 3 | |
Chain K: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-39 | 34 | |
| α-helix | 45-49 | 5 | |
| α-helix | 50-57 | 8 | |
| α-helix | 70-129 | 60 | |
| α-helix | 138-155 | 18 | |
| α-helix | 156-160 | 5 | |
| α-helix | 161-164 | 4 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-186 | 16 | |
| α-helix | 202-210 | 9 | |
| β-strand | 214-218 | 5 | 5 |
| β-strand | 226-230 | 5 | 5 |
Chain L: 10 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-10 | 8 | 6 |
| α-helix | 20-27 | 8 | |
| β-strand | 35-36 | 2 | 6 |
| β-strand | 39 | 1 | 7 |
| α-helix | 44-46 | 3 | |
| β-strand | 52 | 1 | 7 |
| β-strand | 54-59 | 6 | 6 |
| β-strand | 72-77 | 6 | 6 |
| β-strand | 85-89 | 5 | 6 |
| α-helix | 95-107 | 13 | |
| β-strand | 111-113 | 3 | 6 |
| α-helix | 118-127 | 10 | |
| β-strand | 130-132 | 3 | 8 |
| β-strand | 138-140 | 3 | 8 |
| β-strand | 146-149 | 4 | 6 |
| α-helix | 154-156 | 3 | |
| β-strand | 160-164 | 5 | 6 |
| α-helix | 167-177 | 11 | |
| α-helix | 183 | 1 | |
| α-helix | 184-188 | 5 | |
| α-helix | 189-196 | 8 | |
| β-strand | 198 | 1 | 9 |
| β-strand | 205-210 | 6 | 6 |
| β-strand | 214-217 | 4 | 6 |
| β-strand | 220-223 | 4 | 6 |
| α-helix | 230-239 | 10 | |
Chain N: 18 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-24 | 8 | |
| α-helix | 29-42 | 14 | |
| α-helix | 51-63 | 13 | |
| α-helix | 68-74 | 7 | |
| α-helix | 75-79 | 5 | |
| α-helix | 86-99 | 14 | |
| α-helix | 101-103 | 3 | |
| β-strand | 105-113 | 9 | 10 |
| α-helix | 117 | 1 | |
| β-strand | 118 | 1 | 10 |
| α-helix | 119 | 1 | |
| β-strand | 121 | 1 | 11 |
| α-helix | 125-136 | 12 | |
| β-strand | 141-148 | 8 | 10 |
| β-strand | 154-162 | 9 | 10 |
| β-strand | 196 | 1 | 10 |
| β-strand | 200-205 | 6 | 10 |
| β-strand | 208 | 1 | 11 |
| β-strand | 210-214 | 5 | 10 |
| α-helix | 219-233 | 15 | |
| β-strand | 238-242 | 5 | 10 |
| β-strand | 248-249 | 2 | 10 |
| α-helix | 251-257 | 7 | |
| α-helix | 268-270 | 3 | |
| α-helix | 271-275 | 5 | |
| α-helix | 290-293 | 4 | |
| β-strand | 295-298 | 4 | 12 |
| α-helix | 319-334 | 16 | |
| β-strand | 386-392 | 7 | 6 |
| β-strand | 397-405 | 9 | 6 |
| α-helix | 409-418 | 10 | |
| β-strand | 422 | 1 | 9 |
| α-helix | 429-432 | 4 | |
| β-strand | 440-443 | 4 | 6 |
| β-strand | 446-449 | 4 | 6 |
Chain O: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 135-138 | 4 | |
| α-helix | 140-147 | 8 | |
| α-helix | 155-171 | 17 | |
| β-strand | 175-180 | 6 | 13 |
| α-helix | 183-185 | 3 | |
| β-strand | 186-188 | 3 | 14 |
| β-strand | 195-197 | 3 | 14 |
| β-strand | 201-206 | 6 | 13 |
| β-strand | 209-210 | 2 | 15 |
| β-strand | 215-216 | 2 | 15 |
| α-helix | 217-219 | 3 | |
| β-strand | 220-226 | 7 | 13 |
| β-strand | 233-238 | 6 | 13 |
| α-helix | 246-252 | 7 | |
| α-helix | 253-255 | 3 | |
| β-strand | 258 | 1 | 13 |
| α-helix | 261-290 | 30 | |
| β-strand | 298 | 1 | 16 |
| β-strand | 305-309 | 5 | 16 |
| β-strand | 314-320 | 7 | 16 |
| β-strand | 323-329 | 7 | 16 |
| α-helix | 339-347 | 9 | |
| β-strand | 350-351 | 2 | 16 |
| α-helix | 352-363 | 12 | |
7 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 |
|---|
| Centromere-binding protein 1 | A, B | protein | 351 | Saccharomyces cerevisiae | P17106 (AlphaFold model) |
| C0N3 DNA | D | DNA | 153 | Saccharomyces cerevisiae | |
| Inner kinetochore subunit MCM16 | H | protein | 181 | Saccharomyces cerevisiae | Q12262 (AlphaFold model) |
| Inner kinetochore subunit CTF3 | I | protein | 733 | Saccharomyces cerevisiae | Q12748 (AlphaFold model) |
| Inner kinetochore subunit MCM22 | K | protein | 239 | Saccharomyces cerevisiae | P47167 (AlphaFold model) |
| Inner kinetochore subunit IML3 | L | protein | 245 | Saccharomyces cerevisiae | P38265 |
| Inner kinetochore subunit CHL4 | N | protein | 458 | Saccharomyces cerevisiae | P38907 |
| Inner kinetochore subunit MCM21 | O | protein | 368 | Saccharomyces cerevisiae | Q06675 |
| Inner kinetochore subunit CTF19 | P | protein | 369 | Saccharomyces cerevisiae | Q02732 |
| Inner kinetochore subunit OKP1 | Q | protein | 406 | Saccharomyces cerevisiae | P53298 |
| Inner kinetochore subunit CNN1 | T | protein | 361 | Saccharomyces cerevisiae | P43618 |
| Inner kinetochore subunit AME1 | U | protein | 324 | Saccharomyces cerevisiae | P38313 |
4 more molecules are not listed.
Sequence of entity 1 (A, B), FASTA
>8OVW_1 Centromere-binding protein 1 (chains A, B)
MNSLANNNKLSTEDEEIHSARKRGYNEEQNYSEARKKQRDQGLLSQESNDGNIDSALLSE
GATLKGTQSQYESGLTSNKDEKGSDDEDASVAEAAVAATVNYTDLIQGQEDSSDAHTSNQ
TNANGEHKDSLNGERAITPSNEGVKPNTSLEGMTSSPMESTQQSKNDMLIPLAEHDRGPE
HQQDDEDNDDADIDLKKDISMQPGRRGRKPTTLATTDEWKKQRKDSHKEVERRRRENINT
AINVLSDLLPVRESSKAAILACAAEYIQKLKETDEANIEKWTLQKLLSEQNASQLASANE
KLQEELGNAYKEIEYMKRVLRKEGIEYEDMHTHKKQENERKSTRSDNPHEA
Sequence of entity 2 (D), FASTA
>8OVW_2 C0N3 DNA (chains D)
TTCAATGAAATATATATTTCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTA
ATATTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGA
CCAATTGAGCGGCCTCGGCACCATGTGACTTAT
Sequence of entity 3 (H), FASTA
>8OVW_3 Inner kinetochore subunit MCM16 (chains H)
MTNSSEKQWERIQQLEKEHVEVYRELLITLDRLYLIRKHNHAVILSHTQQRLLEIRHQLQ
INLEKTALLIRLLEKPDNTNVLFTKLQNLLEESNSLDYELLQSLGAQSSLHKQLIESRAE
RDELMSKLIELSSKFPKPTIPPDDSDTAGKQVEVEKENETIQELMIALQIHSGYTNISYT
I
Sequence of entity 4 (I), FASTA
>8OVW_4 Inner kinetochore subunit CTF3 (chains I)
MSLILDDIILSLTNANERTPPQALKTTLSLLYEKSKQYGLSSPQLQALVRLLCETSIIDT
VTKVYIVENCFLPDGYLTKELLLEIINHLGTPTVFSRYRIQTPPVLQSALCKWLVHVYFL
FPVHSEREHNISSSIWLHLWQFSFLQKWITPLVIWQATTPVDVKPWKLSIIKRCAMHPGY
RDAPGSATLILQRFQCLVGASSQITESIITINCNRKTLKSHRNLKLDAHFLSILKRILSR
AHPANFPADTVQNTIDMYLSEIHQLGADSIYPLRLQSLPEYVPSDSTVSLWDVTSLEQLA
QNWPQLHIPNDVDYMMKPSLNSNVLLPRKVMSRDSLKHLYSSIILIKNSRDESSSPYEWC
IWQLKRCFAHQIETPQEVIPIIISVSSMDNKLSSRIIQTFCNLKYLKLDELTLKKVCGGI
LPLWKPELISGTREFFVKFMASIFMWSTRDGHDNNCTFSETCFYVLQMITNWVLDDKLIA
LGLTLLHDMQSLLTLDKIFNNATSNRFSTMAFISSLDILTQLSKQTKSDYAIQYLIVGPD
IMNKVFSSDDPLLLSAACRYLVATKNKLMQYPSTNKFVRMQNQYIMDLTNYLYRNKVLSS
KSLFGVSPDFFKQILENLYIPTADFKNAKFFTITGIPALSYICIIILRRLETAENTKIKF
TSGIINEETFNNFFRVHHDEIGQHGWIKGVNNIHDLRVKILMHLSNTANPYRDIAAFLFT
YLKSLSKYSVQNS
Sequence of entity 5 (K), FASTA
>8OVW_5 Inner kinetochore subunit MCM22 (chains K)
MDVEKDVLDVYIKNLENQIGNKRYFLKQAQGAIDEITKRSLDTEGKPVNSEVFTELLRKP
MFFSERADPIGFSLTSNFLSLRAQSSSEWLSLMNDQSVDQKAMLLLQNNINSDLKELLRK
LQHQMTIMDSKKQDHAHIRTRKARNKELWDSLADFLKGYLVPNLDDNDESIDSLTNEVML
LMKRLIEHDLNLTLNDFSSKTIPIYRLLLRANIITVIEGSTNPGTKYIKLIDFNETSLT
Sequence of entity 6 (L), FASTA
>8OVW_6 Inner kinetochore subunit IML3 (chains L)
MPYTWKFLGISKQLSLENGIAKLNQLLNLEVDLDIQTIRVPSDPDGGTAADEYIRYEMRL
DISNLDEGTYSKFIFLGNSKMEVPMFLCYCGTDNRNEVVLQWLKAEYGVIMWPIKFEQKT
MIKLADASIVHVTKENIEQITWFSSKLYFEPETQDKNLRQFSIEIPRESCEGLALGYGNT
MHPYNDAIVPYIYNETGMAVERLPLTSVILAGHTKIMRESIVTSTRSLRNRVLAVVLQSI
QFTSE
Sequence of entity 7 (N), FASTA
>8OVW_7 Inner kinetochore subunit CHL4 (chains N)
MSNELRLEDNYVPTSDTLVVFKQLMKLPVTVLYDLTLSWFAKFGGSFDGDIYLLTETLDL
LIEKGVRRNVIVNRILYVYWPDGLNVFQLAEIDCHLMISKPEKFKWLPSKALRGDGKPYV
VKLQPAKFIENLQTDLAKIYHCHVYMFKHPSLPVLITRIQLFDSNNLFLSTPNIGSINKE
SLYNKLDKFQGKPLISRRPYYVAFPLNSPIIFHSVDKDIYARLVLQSISRTISERETIIF
KPVQKIPVKSIHNIMTLLGPSRFAESMGPWECYASANFERSPLHDYKKHQGLTGKKVMVR
EFDDSFLNDDENFYGKEEPEIRRLRLEKNMIKFKGSANGVMDQKYNDLKEFNEHVHNIRN
GKKNEDSGEPVYISRYSSLVPIEKVGFTLKNEINSRIITIKLKFNGNDIFGGLHELCDKN
LINIDKVPGWLAGENGSFSGTIMNGDFQREQVAKGGLL
Sequence of entity 8 (O), FASTA
>8OVW_8 Inner kinetochore subunit MCM21 (chains O)
MSRIDDLQQDIESLLSEINSLEESREKLKAKIKDKRKNEESANPIVQEFEDLFDQFPQLN
NFLFNEHPELEETDDKDISRAQADIPATPIPYEPKKRAKLENEEILPEQEWVLKTQPMVQ
HQMFDPGVADLLDTDILTSPSKRKRKLKIDDISTSDRSELEDYIVLENVYRMFGITFFPL
VDPIDLKIKDASGEIFVDREMLGIRLEVFSERTSQFEKPHYVLLKKRIKSNSWFLFKHTI
PSFIDVQGIFDDTNGGLVISHDDAYLFAKRVFLQLVEVQKRRQIFKDLEAKKIIHDLDLD
LESSMVSFFVKDIKVELFVKQNEIVSCSILDDIHDFSQNNKSKWEIALLGSLDDLELKLN
HSFATIFK
Sequence of entity 9 (P), FASTA
>8OVW_9 Inner kinetochore subunit CTF19 (chains P)
MDFTSDTTNSHDTSNSHLSLEDAVGTHHAGEADVNIDGDEKQQLSLLDDDQVRALKLQEE
KDALLTRRNTLLQEIQTYQNILMKENNSKTKNGDILQNDITQDFLNLISISSSNPNSAIS
DRKRVERINGLTNLQKELVTKYDTLPLLNMNLRLSYLRDHTYPHLQVSVQSRDRVHNDGI
EVLVVNYKFCRNTMNPFEIQFKMFYKFEDSTLLKWEILRISTNVRLKAKQLLATRNFQKC
LLSLYEFDKIKSKKTGIFQNLINLLKRKTRCYLMNNSDSLIVERVIREGRLTTIKLQINF
IITMPGERGKPRNCFLPMSKISIALWKGGERFNQIDLDEICYGLIKEYGVKTGLKEICNV
CLFPDMYAR
Sequence of entity 10 (Q), FASTA
>8OVW_10 Inner kinetochore subunit OKP1 (chains Q)
MAADRDNFLQNIENDSINNGQAMDLSPNRSSSESDSSILMNVNDIKTLRLDVAPEAKSTQ
SKKSLFYENSDDAEEGEIEERTNKEEGQYHHKGSKQLRFEVGKESTGKLQSHLSDGSATS
GEGNVRPWEFRKVIQAEYRERLPRNYELKHWKKPSKIMIGSILRLLETNTVSALDSVFEK
YEKEMNQMTHGDNNEVKRIYSKKERLLEIILTKIKKKLRQAKFPSRISERDLDIEYIYSK
RQFIQNRYSQELQNNERLEAILSREQNLLEETRKLCMNLKTNNKKRLTEKLIQKDLHPVL
NKAMEYTYGLESTNGFMHPDGPVTFRNDSHELNLMLNDPIKSTADVRLDKEEVLSLLPSL
KEYTKKSKELKETMGQMISDSHEEEIKEVFVPHHESHQDKTEEDIH
Sequence of entity 11 (T), FASTA
>8OVW_11 Inner kinetochore subunit CNN1 (chains T)
MSTPRKAAGNNENTEVSEIRTPFRERALEEQRLKDEVLIRNTPGYRKLLSASTKSHDILN
KDPNEVRSFLQDLSQVLARKSQGNDTTTNKTQARNLIDELAYEESQPEENELLRSRSEKL
TDNNIGNETQPDYTSLSQTVFAKLQERDKGLKSRKIDPIIIQDVPTTGHEDELTVHSPDK
ANSISMEVLRTSPSIGMDQVDEPPVRDPVPISITQQEEPLSEDLPSDDKEETEEAENEDY
SFENTSDENLDDIGNDPIRLNVPAVRRSSIKPLQIMDLKHLTRQFLNENRIILPKQTWST
IQEESLNIMDFLKQKIGTLQKQELVDSFIDMGIINNVDDMFELAHELLPLELQSRIESYL
F
Sequence of entity 12 (U), FASTA
>8OVW_12 Inner kinetochore subunit AME1 (chains U)
MDRDTKLAFRLRGSHSRRTDDIDDDVIVFKTPNAVYREENSPIQSPVQPILSSPKLANSF
EFPITTNNVNAQDRHEHGYQPLDAEDYPMIDSENKSLISESPQNVRNDEDLTTRYNFDDI
PIRQLSSSITSVTTIDVLSSLFINLFENDLIPQALKDFNKSDDDQFRKLLYKLDLRLFQT
ISDQMTRDLKDILDINVSNNELCYQLKQVLARKEDLNQQIISVRNEIQELKAGKDWHDLQ
NEQAKLNDKVKLNKRLNDLTSTLLGKYEGDRKIMSQDSEDDSIRDDSNILDIAHFVDLMD
PYNGLLKKINKINENLSNELQPSL
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 P17106 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7SSA 3.2 Å, Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
- 8OW0 3.4 Å, Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome
- 8OW1 3.7 Å, Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome.
- 10DQ 3.9 Å, Cbf1-CCAN-CEN complex
Browse structure collections
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