6QLF: Inner kinetochore CCAN complex with mask1

Structure of inner kinetochore CCAN complex with mask1. Determined by electron microscopy at 3.45 Å resolution. Released 2 Oct 2019.

Method: Electron microscopy
Resolution: 3.45 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 13,501
Mol. weight: 296.89 kDa
Released: 2 Oct 2019

Explore 6QLF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QLF contains 75 α-helices and 64 β-strands across 8 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 L: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
α-helix	20-27	8
β-strand	32	1	1
β-strand	35-36	2	2
β-strand	39	1	3
β-strand	52	1	3
β-strand	54	1	1
β-strand	55-56	2	2
β-strand	57-59	3	1
β-strand	72-77	6	1
β-strand	85-89	5	1
α-helix	96-107	12
β-strand	113	1	1
α-helix	118-127	10
β-strand	130-131	2	4
β-strand	139-140	2	4
β-strand	146-149	4	5
α-helix	154-156	3
β-strand	158	1	6
β-strand	161-164	4	5
α-helix	167-177	11
α-helix	183	1
α-helix	184-188	5
α-helix	189-196	8
β-strand	198	1	7
β-strand	205-208	4	5
β-strand	214-216	3	1
β-strand	220-223	4	1
α-helix	230-239	10

Chain N: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	17-24	8
α-helix	29-42	14
α-helix	56-64	9
α-helix	68-76	9
α-helix	86-99	14
α-helix	101-103	3
β-strand	106-113	8	8
β-strand	117-118	2	8
α-helix	127-137	11
β-strand	141-146	6	8
β-strand	154-163	10	8
β-strand	195-196	2	8
β-strand	200-205	6	8
β-strand	210-214	5	8
α-helix	219-231	13
β-strand	238-242	5	8
α-helix	247	1
β-strand	248	1	8
α-helix	251-258	8
α-helix	262-264	3
α-helix	269-272	4
α-helix	290-293	4
β-strand	295-298	4	9
α-helix	299-300	2
α-helix	319-333	15
β-strand	384-385	2	10
β-strand	388-391	4	11
β-strand	398-400	3	11
β-strand	404-405	2	10
β-strand	406	1	6
α-helix	409-418	10
β-strand	422	1	7
α-helix	429-432	4
β-strand	440-443	4	11
β-strand	446-449	4	11

Chain O: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	156-171	16
β-strand	175-180	6	12
β-strand	186-188	3	13
β-strand	195-197	3	13
β-strand	201-206	6	12
α-helix	208	1
β-strand	209	1	14
α-helix	210	1
β-strand	216	1	14
β-strand	220-226	7	12
β-strand	233-238	6	12
α-helix	246-252	7
α-helix	253-256	4
β-strand	258	1	12
α-helix	261-290	30
β-strand	298	1	15
β-strand	305-309	5	15
β-strand	314-320	7	15
β-strand	323-330	8	15
α-helix	340-348	9
α-helix	353-359	7

Chain P: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	125-128	4	9
α-helix	134-139	6
α-helix	146-147	2
α-helix	150-155	6
α-helix	156-160	5
β-strand	165	1	16
β-strand	168-172	5	16
β-strand	182-189	8	16
β-strand	197-204	8	16
β-strand	215-220	6	16
α-helix	227-230	4
α-helix	231-233	3
α-helix	237-263	27
β-strand	270-272	3	17
β-strand	279-284	6	17
β-strand	294-303	10	17
β-strand	318-326	9	17
β-strand	331	1	17
α-helix	334-347	14
α-helix	353-362	10

Chain Q: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	163-183	21
α-helix	195-198	4
α-helix	201-216	16
α-helix	234-292	59
α-helix	324-332	9
β-strand	334	1	17
α-helix	338-342	5
α-helix	350-356	7
α-helix	360-381	22
α-helix	383-390	8

Chain U: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	132-155	24
α-helix	171-231	61
α-helix	234-264	31
α-helix	289-298	10
α-helix	306-317	12

Chain Y: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-11	8
α-helix	12-17	6
α-helix	29-31	3
α-helix	36-48	13
α-helix	58-81	24
α-helix	95-102	8
β-strand	108-109	2	15
α-helix	111-117	7
α-helix	137-185	49
α-helix	190-195	6
α-helix	197-213	17
α-helix	224-235	12

Chain Z: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	4-12	9
α-helix	20-23	4
α-helix	40-49	10
α-helix	53-56	4
α-helix	58-80	23
α-helix	89-123	35
α-helix	135-151	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Inner kinetochore subunit IML3	L	protein	245	Saccharomyces cerevisiae	P38265 (AlphaFold model)
Inner kinetochore subunit CHL4	N	protein	464	Saccharomyces cerevisiae	P38907 (AlphaFold model)
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
Inner kinetochore subunit AME1	U	protein	320	Saccharomyces cerevisiae	P38313
Inner kinetochore subunit NKP1	Y	protein	238	Saccharomyces cerevisiae	Q12493
Inner kinetochore subunit NKP2	Z	protein	153	Saccharomyces cerevisiae	Q06162

Sequence of entity 1 (L), FASTA

>6QLF_1 Inner kinetochore subunit IML3 (chains L)
MPYTWKFLGISKQLSLENGIAKLNQLLNLEVDLDIQTIRVPSDPDGGTAADEYIRYEMRL
DISNLDEGTYSKFIFLGNSKMEVPMFLCYCGTDNRNEVVLQWLKAEYGVIMWPIKFEQKT
MIKLADASIVHVTKENIEQITWFSSKLYFEPETQDKNLRQFSIEIPRESCEGLALGYGNT
MHPYNDAIVPYIYNETGMAVERLPLTSVILAGHTKIMRESIVTSTRSLRNRVLAVVLQSI
QFTSE

Sequence of entity 2 (N), FASTA

>6QLF_2 Inner kinetochore subunit CHL4 (chains N)
MSNELRLEDNYVPTSDTLVVFKQLMKLPVTVLYDLTLSWFAKFGGSFDGDIYLLTETLDL
LIEKGVRRNVIVNRILYVYWPDGLNVFQLAEIDCHLMISKPEKFKWLPSKALRGDGKPYV
VKLQPAKFIENLQTDLAKIYHCHVYMFKHPSLPVLITRIQLFDSNNLFLSTPNIGSINKE
SLYNKLDKFQGKPLISRRPYYVAFPLNSPIIFHSVDKDIYARLVLQSISRTISERETIIF
KPVQKIPVKSIHNIMTLLGPSRFAESMGPWECYASANFERSPLHDYKKHQGLTGKKVMVR
EFDDSFLNDDENFYGKEEPEIRRLRLEKNMIKFKGSANGVMDQKYNDLKEFNEHVHNIRN
GKKNEDSGEPVYISRYSSLVPIEKVGFTLKNEINSRIITIKLKFNGNDIFGGLHELCDKN
LINIDKVPGWLAGENGSFSGTIMNGDFQREQVAKGGLLENLYFQ

Sequence of entity 3 (O), FASTA

>6QLF_3 Inner kinetochore subunit MCM21 (chains O)
MSRIDDLQQDIESLLSEINSLEESREKLKAKIKDKRKNEESANPIVQEFEDLFDQFPQLN
NFLFNEHPELEETDDKDISRAQADIPATPIPYEPKKRAKLENEEILPEQEWVLKTQPMVQ
HQMFDPGVADLLDTDILTSPSKRKRKLKIDDISTSDRSELEDYIVLENVYRMFGITFFPL
VDPIDLKIKDASGEIFVDREMLGIRLEVFSERTSQFEKPHYVLLKKRIKSNSWFLFKHTI
PSFIDVQGIFDDTNGGLVISHDDAYLFAKRVFLQLVEVQKRRQIFKDLEAKKIIHDLDLD
LESSMVSFFVKDIKVELFVKQNEIVSCSILDDIHDFSQNNKSKWEIALLGSLDDLELKLN
HSFATIFK

Sequence of entity 4 (P), FASTA

>6QLF_4 Inner kinetochore subunit CTF19 (chains P)
MDFTSDTTNSHDTSNSHLSLEDAVGTHHAGEADVNIDGDEKQQLSLLDDDQVRALKLQEE
KDALLTRRNTLLQEIQTYQNILMKENNSKTKNGDILQNDITQDFLNLISISSSNPNSAIS
DRKRVERINGLTNLQKELVTKYDTLPLLNMNLRLSYLRDHTYPHLQVSVQSRDRVHNDGI
EVLVVNYKFCRNTMNPFEIQFKMFYKFEDSTLLKWEILRISTNVRLKAKQLLATRNFQKC
LLSLYEFDKIKSKKTGIFQNLINLLKRKTRCYLMNNSDSLIVERVIREGRLTTIKLQINF
IITMPGERGKPRNCFLPMSKISIALWKGGERFNQIDLDEICYGLIKEYGVKTGLKEICNV
CLFPDMYAR

Sequence of entity 5 (Q), FASTA

>6QLF_5 Inner kinetochore subunit OKP1 (chains Q)
MAADRDNFLQNIENDSINNGQAMDLSPNRSSSESDSSILMNVNDIKTLRLDVAPEAKSTQ
SKKSLFYENSDDAEEGEIEERTNKEEGQYHHKGSKQLRFEVGKESTGKLQSHLSDGSATS
GEGNVRPWEFRKVIQAEYRERLPRNYELKHWKKPSKIMIGSILRLLETNTVSALDSVFEK
YEKEMNQMTHGDNNEVKRIYSKKERLLEIILTKIKKKLRQAKFPSRISERDLDIEYIYSK
RQFIQNRYSQELQNNERLEAILSREQNLLEETRKLCMNLKTNNKKRLTEKLIQKDLHPVL
NKAMEYTYGLESTNGFMHPDGPVTFRNDSHELNLMLNDPIKSTADVRLDKEEVLSLLPSL
KEYTKKSKELKETMGQMISDSHEEEIKEVFVPHHESHQDKTEEDIH

Sequence of entity 6 (U), FASTA

>6QLF_6 Inner kinetochore subunit AME1 (chains U)
MDRDTKLAFRLRGSHSRRTDDIDDDVIVFKTPNAVYREENSPIQSPVQPILSSPKLANSF
EFPITTNNVNAQDRHEHGYQPLDAEDYPMIDSENKSLISESPQNVRNDEDLTTRYNFDDI
PIRQLSSSITSVTTIDVLSSLFINLFENDLIPQALKDFNKSDDDQFRKLLYKLDLRLFQT
ISDQMTRDLKDILDINVSNNELCYQLKQVLARKEDLNQQIISVRNEIQELKAGKDWHDLQ
NEQAKLNDKVKLNKRLNDLTSTLLGKYEGDRKIMSQDSEDDSIRDDSNILDIAHFVDLMD
PYNGLLKKINKINENLSNEL

Sequence of entity 7 (Y), FASTA

>6QLF_7 Inner kinetochore subunit NKP1 (chains Y)
MTDTYNSISNFIENELTALLSSDDYLMDDLAGELPNEVCRLLKAQVIEKRKDAMSRGKQD
LLSKEIYDNESELRASQSQQIMELVGDIPKYSLGSELRNRVEGEPQSTSIERLIEDVLKL
PQMEVADEEEVEVENDLKVLSEYSNLRKDLILKCQALQIGESKLSDILSQTNSINSLTTS
IKEASEDDDISEYFATYNGKLVVALEEMKLLLEEAVKTFGNSPEKREKIKKILSELKK

Sequence of entity 8 (Z), FASTA

>6QLF_8 Inner kinetochore subunit NKP2 (chains Z)
MNSEQLLHNYVSDSLLTTLISFQEFKQQLQSYTSDEQQLQHWYELLQARDARVTSELEAR
IKQFFITLRSRLLRFLESEQLSHSLSLETLIDALYKINDLLQQRLQILDDAIQEKTSELA
EFENMVRSPSAGDNAIPGLLQIIQSYINLLEEN

Primary citation

Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Yan, K., Yang, J., Zhang, Z. et al. Nature (2019) 574:278-282. DOI 10.1038/s41586-019-1609-1 · PubMed

Other PDB entries of the same protein (UniProt P38265 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JE3 2.28 Å, An Iml3-Chl4 heterodimer links the core centromere to factors required for accurate…
4IT3 2.5 Å, Crystal Structure of Iml3 from S. cerevisiae
4KR1 2.5 Å, Crystal structure of the kinetechore protein Iml3 from budding yeast
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
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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