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
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

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