8OVX: Yeast CENP-OPQU+

Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus. Determined by electron microscopy at 3.4 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 6,763
Mol. weight: 215.69 kDa
Released: 9 Aug 2023

Explore 8OVX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OVX contains 37 α-helices and 22 β-strands across 6 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 O: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	163-171	9
β-strand	175-179	5	1
β-strand	202-206	5	1
β-strand	209	1	2
β-strand	216	1	2
α-helix	218-219	2
β-strand	220-226	7	1
β-strand	233-238	6	1
α-helix	254-256	3
α-helix	261-290	30
β-strand	297-298	2	3
β-strand	307-308	2	3
β-strand	315-320	6	4
β-strand	323-329	7	4
α-helix	354-363	10

Chain P: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	154-159	6
β-strand	165-174	10	5
β-strand	181-189	9	5
β-strand	197-205	9	5
β-strand	215-220	6	5
α-helix	227-230	4
α-helix	231-233	3
α-helix	237-239	3
α-helix	245-262	18
β-strand	270-273	4	6
β-strand	279-284	6	6
β-strand	294-303	10	6
α-helix	304-306	3
β-strand	318-326	9	6
β-strand	331	1	6
α-helix	334-347	14
α-helix	350-362	13

Chain Q: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	278-290	13
α-helix	322-331	10
β-strand	334	1	6
α-helix	338-342	5
α-helix	350-356	7
α-helix	359-379	21
α-helix	383-390	8

Chain U: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	234-265	32
α-helix	287-298	12
α-helix	306-320	15

Chain Y: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-30	29
β-strand	31	1	7
β-strand	34	1	7
α-helix	36-45	10
α-helix	46-50	5
α-helix	51-53	3
α-helix	56-85	30
α-helix	111-118	8
α-helix	138-185	48
α-helix	190-193	4
α-helix	197-218	22
α-helix	222-237	16

Chain Z: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-12	10
α-helix	22-28	7
α-helix	38-70	33
α-helix	89-125	37
α-helix	132-152	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Inner kinetochore subunit MCM21	O	protein	368	Saccharomyces cerevisiae	Q06675 (AlphaFold model)
Inner kinetochore subunit CTF19	P	protein	369	Saccharomyces cerevisiae	Q02732 (AlphaFold model)
Inner kinetochore subunit OKP1	Q	protein	406	Saccharomyces cerevisiae	P53298 (AlphaFold model)
Inner kinetochore subunit AME1	U	protein	324	Saccharomyces cerevisiae	P38313 (AlphaFold model)
Inner kinetochore subunit NKP1	Y	protein	238	Saccharomyces cerevisiae	Q12493
Inner kinetochore subunit NKP2	Z	protein	153	Saccharomyces cerevisiae	Q06162

Sequence of entity 1 (O), FASTA

>8OVX_1 Inner kinetochore subunit MCM21 (chains O)
MSRIDDLQQDIESLLSEINSLEESREKLKAKIKDKRKNEESANPIVQEFEDLFDQFPQLN
NFLFNEHPELEETDDKDISRAQADIPATPIPYEPKKRAKLENEEILPEQEWVLKTQPMVQ
HQMFDPGVADLLDTDILTSPSKRKRKLKIDDISTSDRSELEDYIVLENVYRMFGITFFPL
VDPIDLKIKDASGEIFVDREMLGIRLEVFSERTSQFEKPHYVLLKKRIKSNSWFLFKHTI
PSFIDVQGIFDDTNGGLVISHDDAYLFAKRVFLQLVEVQKRRQIFKDLEAKKIIHDLDLD
LESSMVSFFVKDIKVELFVKQNEIVSCSILDDIHDFSQNNKSKWEIALLGSLDDLELKLN
HSFATIFK

Sequence of entity 2 (P), FASTA

>8OVX_2 Inner kinetochore subunit CTF19 (chains P)
MDFTSDTTNSHDTSNSHLSLEDAVGTHHAGEADVNIDGDEKQQLSLLDDDQVRALKLQEE
KDALLTRRNTLLQEIQTYQNILMKENNSKTKNGDILQNDITQDFLNLISISSSNPNSAIS
DRKRVERINGLTNLQKELVTKYDTLPLLNMNLRLSYLRDHTYPHLQVSVQSRDRVHNDGI
EVLVVNYKFCRNTMNPFEIQFKMFYKFEDSTLLKWEILRISTNVRLKAKQLLATRNFQKC
LLSLYEFDKIKSKKTGIFQNLINLLKRKTRCYLMNNSDSLIVERVIREGRLTTIKLQINF
IITMPGERGKPRNCFLPMSKISIALWKGGERFNQIDLDEICYGLIKEYGVKTGLKEICNV
CLFPDMYAR

Sequence of entity 3 (Q), FASTA

>8OVX_3 Inner kinetochore subunit OKP1 (chains Q)
MAADRDNFLQNIENDSINNGQAMDLSPNRSSSESDSSILMNVNDIKTLRLDVAPEAKSTQ
SKKSLFYENSDDAEEGEIEERTNKEEGQYHHKGSKQLRFEVGKESTGKLQSHLSDGSATS
GEGNVRPWEFRKVIQAEYRERLPRNYELKHWKKPSKIMIGSILRLLETNTVSALDSVFEK
YEKEMNQMTHGDNNEVKRIYSKKERLLEIILTKIKKKLRQAKFPSRISERDLDIEYIYSK
RQFIQNRYSQELQNNERLEAILSREQNLLEETRKLCMNLKTNNKKRLTEKLIQKDLHPVL
NKAMEYTYGLESTNGFMHPDGPVTFRNDSHELNLMLNDPIKSTADVRLDKEEVLSLLPSL
KEYTKKSKELKETMGQMISDSHEEEIKEVFVPHHESHQDKTEEDIH

Sequence of entity 4 (U), FASTA

>8OVX_4 Inner kinetochore subunit AME1 (chains U)
MDRDTKLAFRLRGSHSRRTDDIDDDVIVFKTPNAVYREENSPIQSPVQPILSSPKLANSF
EFPITTNNVNAQDRHEHGYQPLDAEDYPMIDSENKSLISESPQNVRNDEDLTTRYNFDDI
PIRQLSSSITSVTTIDVLSSLFINLFENDLIPQALKDFNKSDDDQFRKLLYKLDLRLFQT
ISDQMTRDLKDILDINVSNNELCYQLKQVLARKEDLNQQIISVRNEIQELKAGKDWHDLQ
NEQAKLNDKVKLNKRLNDLTSTLLGKYEGDRKIMSQDSEDDSIRDDSNILDIAHFVDLMD
PYNGLLKKINKINENLSNELQPSL

Sequence of entity 5 (Y), FASTA

>8OVX_5 Inner kinetochore subunit NKP1 (chains Y)
MTDTYNSISNFIENELTALLSSDDYLMDDLAGELPNEVCRLLKAQVIEKRKDAMSRGKQD
LLSKEIYDNESELRASQSQQIMELVGDIPKYSLGSELRNRVEGEPQSTSIERLIEDVLKL
PQMEVADEEEVEVENDLKVLSEYSNLRKDLILKCQALQIGESKLSDILSQTNSINSLTTS
IKEASEDDDISEYFATYNGKLVVALEEMKLLLEEAVKTFGNSPEKREKIKKILSELKK

Sequence of entity 6 (Z), FASTA

>8OVX_6 Inner kinetochore subunit NKP2 (chains Z)
MNSEQLLHNYVSDSLLTTLISFQEFKQQLQSYTSDEQQLQHWYELLQARDARVTSELEAR
IKQFFITLRSRLLRFLESEQLSHSLSLETLIDALYKINDLLQQRLQILDDAIQEKTSELA
EFENMVRSPSAGDNAIPGLLQIIQSYINLLEEN

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 Q06675 (AlphaFold model), which also has an AlphaFold model), best resolution first:

10FI 3.3 Å, apo CCAN purified from budding yeast
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
6QLF 3.45 Å, Structure of inner kinetochore CCAN complex with mask1
6QLE 3.55 Å, Structure of inner kinetochore CCAN complex
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
6QLD 4.15 Å, Structure of inner kinetochore CCAN-Cenp-A complex
6NUW 4.25 Å, Yeast Ctf19 complex
10JC 6.5 Å, CCAN dimer purified from budding yeast

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