8OW1: Yeast Inner kinetochore
Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Determined by electron microscopy at 3.7 Å resolution. Released 9 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 42
- Atoms
- 78,671
- Mol. weight
- 1490.63 kDa
- Released
- 9 Aug 2023
Explore 8OW1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OW1 contains 436 α-helices and 166 β-strands across 40 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 | 134-146 | 13 | |
| α-helix | 155-168 | 14 | |
| β-strand | 177 | 1 | 12 |
| α-helix | 180-207 | 28 | |
| β-strand | 212-213 | 2 | 11 |
| α-helix | 215-225 | 11 | |
Chain A: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 227-247 | 21 | |
| α-helix | 256-323 | 68 | |
Chain b: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-42 | 11 | |
| β-strand | 46-47 | 2 | 11 |
| α-helix | 51-76 | 26 | |
| β-strand | 81 | 1 | 12 |
| α-helix | 84-94 | 11 | |
| β-strand | 98 | 1 | 13 |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 219-248 | 30 | |
| α-helix | 256-323 | 68 | |
Chain c: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 30-38 | 9 | |
| β-strand | 44 | 1 | 17 |
| α-helix | 48-74 | 27 | |
| α-helix | 82-91 | 10 | |
| α-helix | 93-98 | 6 | |
| β-strand | 103 | 1 | 25 |
Chain ce: 33 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-68 | 11 | |
| α-helix | 69-79 | 11 | |
| α-helix | 89-91 | 3 | |
| α-helix | 97-103 | 7 | |
| α-helix | 110-121 | 12 | |
| α-helix | 123-128 | 6 | |
| α-helix | 134-145 | 12 | |
| β-strand | 153 | 1 | 18 |
| α-helix | 154-173 | 20 | |
| α-helix | 176-182 | 7 | |
| α-helix | 186-189 | 4 | |
| α-helix | 204-223 | 20 | |
| α-helix | 231-241 | 11 | |
| α-helix | 245-248 | 4 | |
| α-helix | 250-265 | 16 | |
| α-helix | 280-302 | 23 | |
| β-strand | 305 | 1 | 19 |
| β-strand | 308 | 1 | 19 |
| α-helix | 315-317 | 3 | |
| α-helix | 341-356 | 16 | |
| α-helix | 364-366 | 3 | |
| α-helix | 367-386 | 20 | |
| α-helix | 394-417 | 24 | |
| α-helix | 418-422 | 5 | |
| α-helix | 427-447 | 21 | |
| α-helix | 451-455 | 5 | |
| α-helix | 457-474 | 18 | |
| α-helix | 480-494 | 15 | |
| α-helix | 498-500 | 3 | |
| α-helix | 502-515 | 14 | |
| α-helix | 517-523 | 7 | |
| α-helix | 525-526 | 2 | |
| β-strand | 527-528 | 2 | 20 |
| β-strand | 533-534 | 2 | 20 |
| α-helix | 536-552 | 17 | |
| α-helix | 555-561 | 7 | |
| α-helix | 566-567 | 2 | |
| α-helix | 590-600 | 11 | |
Chain CE: 30 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-36 | 6 | |
| α-helix | 40-44 | 5 | |
| α-helix | 57-69 | 13 | |
| α-helix | 70-74 | 5 | |
| β-strand | 89 | 1 | 18 |
| α-helix | 90-91 | 2 | |
| α-helix | 97-105 | 9 | |
| α-helix | 108-117 | 10 | |
| α-helix | 134-148 | 15 | |
| α-helix | 154-173 | 20 | |
| α-helix | 176-182 | 7 | |
| α-helix | 186-192 | 7 | |
| α-helix | 204-223 | 20 | |
| α-helix | 232-240 | 9 | |
| α-helix | 245-248 | 4 | |
| α-helix | 250-264 | 15 | |
| α-helix | 280-302 | 23 | |
| α-helix | 340-360 | 21 | |
| α-helix | 367-370 | 4 | |
| α-helix | 372-382 | 11 | |
| α-helix | 394-422 | 29 | |
| α-helix | 425-444 | 20 | |
| α-helix | 453-455 | 3 | |
| α-helix | 459-474 | 16 | |
| α-helix | 480-494 | 15 | |
| α-helix | 502-523 | 22 | |
| α-helix | 525-526 | 2 | |
| β-strand | 527-528 | 2 | 29 |
| β-strand | 533-534 | 2 | 29 |
| α-helix | 536-551 | 16 | |
| α-helix | 555-562 | 8 | |
| α-helix | 591-600 | 10 | |
| α-helix | 603-605 | 3 | |
Chain CT: 18 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 14-24 | 11 | |
| α-helix | 61 | 1 | |
| α-helix | 62-66 | 5 | |
| α-helix | 67-69 | 3 | |
| α-helix | 76-79 | 4 | |
| α-helix | 81-93 | 13 | |
| α-helix | 98-109 | 12 | |
| β-strand | 119-120 | 2 | 14 |
| β-strand | 129-132 | 4 | 14 |
| β-strand | 138-142 | 5 | 14 |
| α-helix | 144-150 | 7 | |
| β-strand | 169-170 | 2 | 14 |
| α-helix | 177-188 | 12 | |
| β-strand | 198-201 | 4 | 14 |
| α-helix | 258-263 | 6 | |
| β-strand | 275-279 | 5 | 14 |
| α-helix | 281-287 | 7 | |
| α-helix | 305-308 | 4 | |
| β-strand | 311-319 | 9 | 14 |
| β-strand | 326-327 | 2 | 15 |
| β-strand | 336-346 | 11 | 14 |
| β-strand | 350-351 | 2 | 15 |
| β-strand | 358-362 | 5 | 14 |
| β-strand | 366-368 | 3 | 14 |
| α-helix | 373-380 | 8 | |
| α-helix | 384-387 | 4 | |
| β-strand | 392 | 1 | 16 |
| α-helix | 401-403 | 3 | |
| β-strand | 410-413 | 4 | 16 |
| α-helix | 421-433 | 13 | |
| β-strand | 440-444 | 5 | 14 |
| β-strand | 448-449 | 2 | 14 |
| β-strand | 454-455 | 2 | 16 |
| α-helix | 457-461 | 5 | |
| β-strand | 465-468 | 4 | 14 |
| β-strand | 475-478 | 4 | 16 |
32 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) |
| Inner kinetochore subunit CTF3 | I, II | protein | 733 | Saccharomyces cerevisiae | Q12748 (AlphaFold model) |
| Inner kinetochore subunit MCM22 | K, KK | protein | 239 | Saccharomyces cerevisiae | P47167 (AlphaFold model) |
| Inner kinetochore subunit MCM16 | H, HH | protein | 181 | Saccharomyces cerevisiae | Q12262 (AlphaFold model) |
| Inner kinetochore subunit IML3 | L, LL | protein | 245 | Saccharomyces cerevisiae | P38265 |
| Inner kinetochore subunit CHL4 | N, NN | protein | 458 | Saccharomyces cerevisiae | P38907 |
| Centromere DNA-binding protein complex CBF3 subunit C | CT | protein | 478 | Saccharomyces cerevisiae | P35203 |
| Centromere DNA-binding protein complex CBF3 subunit B | CE, ce | protein | 608 | Saccharomyces cerevisiae | P40969 |
| Suppressor of kinetochore protein 1 | SK | protein | 194 | Saccharomyces cerevisiae | P52286 |
| Inner kinetochore subunit CTF19 | P, PP | protein | 369 | Saccharomyces cerevisiae | Q02732 |
| Inner kinetochore subunit OKP1 | Q, QQ | protein | 406 | Saccharomyces cerevisiae | P53298 |
| Inner kinetochore subunit MCM21 | O, OO | protein | 368 | Saccharomyces cerevisiae | Q06675 |
11 more molecules are not listed.
Sequence of entity 1 (A, B), FASTA
>8OW1_1 Centromere-binding protein 1 (chains A, B)
MNSLANNNKLSTEDEEIHSARKRGYNEEQNYSEARKKQRDQGLLSQESNDGNIDSALLSE
GATLKGTQSQYESGLTSNKDEKGSDDEDASVAEAAVAATVNYTDLIQGQEDSSDAHTSNQ
TNANGEHKDSLNGERAITPSNEGVKPNTSLEGMTSSPMESTQQSKNDMLIPLAEHDRGPE
HQQDDEDNDDADIDLKKDISMQPGRRGRKPTTLATTDEWKKQRKDSHKEVERRRRENINT
AINVLSDLLPVRESSKAAILACAAEYIQKLKETDEANIEKWTLQKLLSEQNASQLASANE
KLQEELGNAYKEIEYMKRVLRKEGIEYEDMHTHKKQENERKSTRSDNPHEA
Sequence of entity 2 (I, II), FASTA
>8OW1_2 Inner kinetochore subunit CTF3 (chains I, II)
MSLILDDIILSLTNANERTPPQALKTTLSLLYEKSKQYGLSSPQLQALVRLLCETSIIDT
VTKVYIVENCFLPDGYLTKELLLEIINHLGTPTVFSRYRIQTPPVLQSALCKWLVHVYFL
FPVHSEREHNISSSIWLHLWQFSFLQKWITPLVIWQATTPVDVKPWKLSIIKRCAMHPGY
RDAPGSATLILQRFQCLVGASSQITESIITINCNRKTLKSHRNLKLDAHFLSILKRILSR
AHPANFPADTVQNTIDMYLSEIHQLGADSIYPLRLQSLPEYVPSDSTVSLWDVTSLEQLA
QNWPQLHIPNDVDYMMKPSLNSNVLLPRKVMSRDSLKHLYSSIILIKNSRDESSSPYEWC
IWQLKRCFAHQIETPQEVIPIIISVSSMDNKLSSRIIQTFCNLKYLKLDELTLKKVCGGI
LPLWKPELISGTREFFVKFMASIFMWSTRDGHDNNCTFSETCFYVLQMITNWVLDDKLIA
LGLTLLHDMQSLLTLDKIFNNATSNRFSTMAFISSLDILTQLSKQTKSDYAIQYLIVGPD
IMNKVFSSDDPLLLSAACRYLVATKNKLMQYPSTNKFVRMQNQYIMDLTNYLYRNKVLSS
KSLFGVSPDFFKQILENLYIPTADFKNAKFFTITGIPALSYICIIILRRLETAENTKIKF
TSGIINEETFNNFFRVHHDEIGQHGWIKGVNNIHDLRVKILMHLSNTANPYRDIAAFLFT
YLKSLSKYSVQNS
Sequence of entity 3 (K, KK), FASTA
>8OW1_3 Inner kinetochore subunit MCM22 (chains K, KK)
MDVEKDVLDVYIKNLENQIGNKRYFLKQAQGAIDEITKRSLDTEGKPVNSEVFTELLRKP
MFFSERADPIGFSLTSNFLSLRAQSSSEWLSLMNDQSVDQKAMLLLQNNINSDLKELLRK
LQHQMTIMDSKKQDHAHIRTRKARNKELWDSLADFLKGYLVPNLDDNDESIDSLTNEVML
LMKRLIEHDLNLTLNDFSSKTIPIYRLLLRANIITVIEGSTNPGTKYIKLIDFNETSLT
Sequence of entity 4 (H, HH), FASTA
>8OW1_4 Inner kinetochore subunit MCM16 (chains H, HH)
MTNSSEKQWERIQQLEKEHVEVYRELLITLDRLYLIRKHNHAVILSHTQQRLLEIRHQLQ
INLEKTALLIRLLEKPDNTNVLFTKLQNLLEESNSLDYELLQSLGAQSSLHKQLIESRAE
RDELMSKLIELSSKFPKPTIPPDDSDTAGKQVEVEKENETIQELMIALQIHSGYTNISYT
I
Sequence of entity 5 (L, LL), FASTA
>8OW1_5 Inner kinetochore subunit IML3 (chains L, LL)
MPYTWKFLGISKQLSLENGIAKLNQLLNLEVDLDIQTIRVPSDPDGGTAADEYIRYEMRL
DISNLDEGTYSKFIFLGNSKMEVPMFLCYCGTDNRNEVVLQWLKAEYGVIMWPIKFEQKT
MIKLADASIVHVTKENIEQITWFSSKLYFEPETQDKNLRQFSIEIPRESCEGLALGYGNT
MHPYNDAIVPYIYNETGMAVERLPLTSVILAGHTKIMRESIVTSTRSLRNRVLAVVLQSI
QFTSE
Sequence of entity 6 (N, NN), FASTA
>8OW1_6 Inner kinetochore subunit CHL4 (chains N, NN)
MSNELRLEDNYVPTSDTLVVFKQLMKLPVTVLYDLTLSWFAKFGGSFDGDIYLLTETLDL
LIEKGVRRNVIVNRILYVYWPDGLNVFQLAEIDCHLMISKPEKFKWLPSKALRGDGKPYV
VKLQPAKFIENLQTDLAKIYHCHVYMFKHPSLPVLITRIQLFDSNNLFLSTPNIGSINKE
SLYNKLDKFQGKPLISRRPYYVAFPLNSPIIFHSVDKDIYARLVLQSISRTISERETIIF
KPVQKIPVKSIHNIMTLLGPSRFAESMGPWECYASANFERSPLHDYKKHQGLTGKKVMVR
EFDDSFLNDDENFYGKEEPEIRRLRLEKNMIKFKGSANGVMDQKYNDLKEFNEHVHNIRN
GKKNEDSGEPVYISRYSSLVPIEKVGFTLKNEINSRIITIKLKFNGNDIFGGLHELCDKN
LINIDKVPGWLAGENGSFSGTIMNGDFQREQVAKGGLL
Sequence of entity 7 (CT), FASTA
>8OW1_7 Centromere DNA-binding protein complex CBF3 subunit C (chains CT)
MPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSK
KLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEW
TYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQLV
DKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASKR
SHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKT
ISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLT
MKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEINQ
ITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVI
Sequence of entity 8 (CE, ce), FASTA
>8OW1_8 Centromere DNA-binding protein complex CBF3 subunit B (chains CE, ce)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPD
LLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAME
NLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLA
EIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLIL
ATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCD
YLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLN
KSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLI
YYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESA
AVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKI
LQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSE
YNISDILS
Sequence of entity 9 (SK), FASTA
>8OW1_9 Suppressor of kinetochore protein 1 (chains SK)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR
Sequence of entity 10 (P, PP), FASTA
>8OW1_10 Inner kinetochore subunit CTF19 (chains P, PP)
MDFTSDTTNSHDTSNSHLSLEDAVGTHHAGEADVNIDGDEKQQLSLLDDDQVRALKLQEE
KDALLTRRNTLLQEIQTYQNILMKENNSKTKNGDILQNDITQDFLNLISISSSNPNSAIS
DRKRVERINGLTNLQKELVTKYDTLPLLNMNLRLSYLRDHTYPHLQVSVQSRDRVHNDGI
EVLVVNYKFCRNTMNPFEIQFKMFYKFEDSTLLKWEILRISTNVRLKAKQLLATRNFQKC
LLSLYEFDKIKSKKTGIFQNLINLLKRKTRCYLMNNSDSLIVERVIREGRLTTIKLQINF
IITMPGERGKPRNCFLPMSKISIALWKGGERFNQIDLDEICYGLIKEYGVKTGLKEICNV
CLFPDMYAR
Sequence of entity 11 (Q, QQ), FASTA
>8OW1_11 Inner kinetochore subunit OKP1 (chains Q, QQ)
MAADRDNFLQNIENDSINNGQAMDLSPNRSSSESDSSILMNVNDIKTLRLDVAPEAKSTQ
SKKSLFYENSDDAEEGEIEERTNKEEGQYHHKGSKQLRFEVGKESTGKLQSHLSDGSATS
GEGNVRPWEFRKVIQAEYRERLPRNYELKHWKKPSKIMIGSILRLLETNTVSALDSVFEK
YEKEMNQMTHGDNNEVKRIYSKKERLLEIILTKIKKKLRQAKFPSRISERDLDIEYIYSK
RQFIQNRYSQELQNNERLEAILSREQNLLEETRKLCMNLKTNNKKRLTEKLIQKDLHPVL
NKAMEYTYGLESTNGFMHPDGPVTFRNDSHELNLMLNDPIKSTADVRLDKEEVLSLLPSL
KEYTKKSKELKETMGQMISDSHEEEIKEVFVPHHESHQDKTEEDIH
Sequence of entity 12 (O, OO), FASTA
>8OW1_12 Inner kinetochore subunit MCM21 (chains O, OO)
MSRIDDLQQDIESLLSEINSLEESREKLKAKIKDKRKNEESANPIVQEFEDLFDQFPQLN
NFLFNEHPELEETDDKDISRAQADIPATPIPYEPKKRAKLENEEILPEQEWVLKTQPMVQ
HQMFDPGVADLLDTDILTSPSKRKRKLKIDDISTSDRSELEDYIVLENVYRMFGITFFPL
VDPIDLKIKDASGEIFVDREMLGIRLEVFSERTSQFEKPHYVLLKKRIKSNSWFLFKHTI
PSFIDVQGIFDDTNGGLVISHDDAYLFAKRVFLQLVEVQKRRQIFKDLEAKKIIHDLDLD
LESSMVSFFVKDIKVELFVKQNEIVSCSILDDIHDFSQNNKSKWEIALLGSLDDLELKLN
HSFATIFK
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
- 8OVW 3.4 Å, Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA
- 8OW0 3.4 Å, Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome
- 10DQ 3.9 Å, Cbf1-CCAN-CEN complex
Browse structure collections
About this viewer
MolViewer shows 8OW1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.