6QLE: Inner kinetochore CCAN complex

Structure of inner kinetochore CCAN complex. Determined by electron microscopy at 3.55 Å resolution. Released 2 Oct 2019.

Method: Electron microscopy
Resolution: 3.55 Å
Organism: Saccharomyces cerevisiae
Chains: 11
Atoms: 18,162
Mol. weight: 350.59 kDa
Released: 2 Oct 2019

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

Secondary structure: helices and β-sheets

6QLE contains 97 α-helices and 67 β-strands across 11 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 H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-38	33
α-helix	47-72	26
α-helix	84-93	10
α-helix	97-134	38

Chain I: 22 helices, 0 β-strands

Element	Residues	Length
α-helix	324-327	4
α-helix	336-338	3
α-helix	341-349	9
α-helix	355-368	14
α-helix	375-377	3
α-helix	379-386	8
α-helix	390-400	11
α-helix	410-420	11
α-helix	421-423	3
α-helix	432-447	16
α-helix	458-472	15
α-helix	479-492	14
α-helix	507-523	17
α-helix	539-547	9
α-helix	551-568	18
α-helix	577-591	15
α-helix	608-618	11
α-helix	640-652	13
α-helix	667-674	8
α-helix	694-706	13
α-helix	713-720	8
α-helix	723-725	3

Chain K: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-39	31
α-helix	51-58	8
α-helix	71-127	57

Chain L: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
α-helix	20-27	8
β-strand	31-33	3	2
β-strand	38-39	2	3
β-strand	52-53	2	3
β-strand	58-60	3	2
β-strand	73-76	4	1
β-strand	85-89	5	1
α-helix	95-107	13
β-strand	113	1	1
α-helix	118-126	9
β-strand	130-132	3	4
β-strand	138-140	3	4
β-strand	146	1	5
β-strand	149	1	6
α-helix	154-156	3
β-strand	158	1	7
β-strand	161	1	6
β-strand	164	1	5
α-helix	167-177	11
α-helix	183-186	4
α-helix	189-196	8
β-strand	198	1	8
β-strand	205	1	6
β-strand	209	1	5
β-strand	215-216	2	1
β-strand	220-222	3	1
α-helix	230-239	10

Chain N: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	17-24	8
α-helix	29-42	14
α-helix	56-59	4
α-helix	61-64	4
α-helix	68-76	9
α-helix	86-99	14
α-helix	101-103	3
β-strand	106-113	8	9
β-strand	118	1	9
α-helix	127-136	10
β-strand	141-148	8	9
β-strand	154-163	10	9
β-strand	195-196	2	9
β-strand	200-205	6	9
β-strand	210-214	5	9
α-helix	219-231	13
β-strand	238-242	5	9
β-strand	248	1	9
α-helix	251-258	8
α-helix	262-264	3
α-helix	290-293	4
β-strand	295-298	4	10
α-helix	299-301	3
α-helix	319-333	15
β-strand	385	1	11
β-strand	388-392	5	12
β-strand	397-400	4	12
β-strand	404	1	11
β-strand	406	1	7
α-helix	409-418	10
β-strand	422	1	8
α-helix	429-432	4
β-strand	440-443	4	12
β-strand	446-449	4	12

Chain O: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	155-171	17
β-strand	175-180	6	13
β-strand	186-188	3	14
β-strand	195-197	3	14
β-strand	201-206	6	13
α-helix	208	1
β-strand	209	1	15
α-helix	210	1
β-strand	216	1	15
β-strand	220-226	7	13
β-strand	233-238	6	13
α-helix	246-252	7
α-helix	253-256	4
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	323-330	8	16
α-helix	340-348	9
β-strand	351	1	16
α-helix	353-358	6

Chain P: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	98-108	11
β-strand	125-128	4	10
α-helix	134-139	6
β-strand	146	1	13
α-helix	150-155	6
α-helix	156-160	5
β-strand	168-172	5	17
β-strand	175	1	18
β-strand	180	1	18
β-strand	182-189	8	17
β-strand	197-204	8	17
β-strand	215-220	6	17
α-helix	231-233	3
α-helix	237-263	27
β-strand	270-272	3	19
β-strand	279-284	6	19
β-strand	294-303	10	19
β-strand	318-326	9	19
β-strand	331	1	19
α-helix	334-347	14
α-helix	354-362	9

Chain Q: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	127-136	10
α-helix	162-186	25
α-helix	194-216	23
α-helix	234-290	57
α-helix	324-331	8
β-strand	334	1	19
α-helix	338-342	5
α-helix	350-356	7
α-helix	359-381	23
α-helix	383-386	4

3 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
Central kinetochore subunit MCM16,Central kinetochore subunit MCM16,Inner kinetochore subunit…	H	protein	181	Saccharomyces cerevisiae	Q12262 (AlphaFold model)
Central kinetochore subunit CTF3,Inner kinetochore subunit CTF3,Central kinetochore subunit…	I	protein	412	Saccharomyces cerevisiae	Q12748 (AlphaFold model)
Inner kinetochore subunit MCM22,Inner kinetochore subunit MCM22,Inner kinetochore subunit…	K	protein	204	Saccharomyces cerevisiae	P47167 (AlphaFold model)
Inner kinetochore subunit IML3	L	protein	245	Saccharomyces cerevisiae	P38265 (AlphaFold model)
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,Inner kinetochore subunit OKP1,Inner kinetochore subunit OKP1,Inner…	Q	protein	261	Saccharomyces cerevisiae	P53298
Inner kinetochore subunit AME1,Inner kinetochore subunit AME1,Inner kinetochore subunit AME1,Inner…	U	protein	186	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 (H), FASTA

>6QLE_1 Central kinetochore subunit MCM16,Central kinetochore subunit MCM16,Inner kinetochore subunit MCM16,Mcm16p (chains H)
MTNSSEKQWERIQQLEKEHVEVYRELLITLDRLYLIRRHNHAVILSHTQQRLLEIRHQLQ
INLEKTALLIRLLEKPDNTNVLFTKLQNLLEESNSLDYELLQSLGAQSSLHKQLIESRAE
RDELMSKLIELSSKFPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
X

Sequence of entity 2 (I), FASTA

>6QLE_2 Central kinetochore subunit CTF3,Inner kinetochore subunit CTF3,Central kinetochore subunit CTF3,Inner kinetochore subunit CTF3 (chains I)
XXXXXXXXXXXSLKHLYSSIILIKNSRDESSSPYEWCIWQLKRCFAHQIETPQEVIPIII
SVSSMDNKLSSRIIQTFCNLKYLKLDELTLKKVCGGILPLWKPELISGTREFFVKFMASI
FMWSTRDGHDNNCTFSETCFYVLQMITNWVLDDKLIALGLTLLHDMQSLLTLDKIFNNAT
SNRFSTMAFISSLDILTQLSKQTKSDYAIQYLIVGPDIMNKVFSSDDPLLLSAACRYLVA
TKNKLMQYPSTNKFVRMQNQYIMDLTNYLYRNKVLSSKSLFGVSPDFFKQILENLYIPTA
DFKNAKFFTITGIPALSYICIIILRRLETAENTXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXVNNIHDLRVKILMHLSNTANPYRDIAAFLFTYLKSLSKYSVQNS

Sequence of entity 3 (K), FASTA

>6QLE_3 Inner kinetochore subunit MCM22,Inner kinetochore subunit MCM22,Inner kinetochore subunit MCM22,Inner kinetochore subunit MCM22 (chains K)
MDVEKDVLDVYIKNLENQIGNKRYFLKQAQGAIDEITKRSLDTEGKPVNSEVFTELLRKP
MFFSERADPIGFSLTSNFLSLRAQSSSEWLSLMNDQSVDQKAMLLLQNNINSDLKELLRK
LQHQMTIMDSKKQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 4 (L), FASTA

>6QLE_4 Inner kinetochore subunit IML3 (chains L)
MPYTWKFLGISKQLSLENGIAKLNQLLNLEVDLDIQTIRVPSDPDGGTAADEYIRYEMRL
DISNLDEGTYSKFIFLGNSKMEVPMFLCYCGTDNRNEVVLQWLKAEYGVIMWPIKFEQKT
MIKLADASIVHVTKENIEQITWFSSKLYFEPETQDKNLRQFSIEIPRESCEGLALGYGNT
MHPYNDAIVPYIYNETGMAVERLPLTSVILAGHTKIMRESIVTSTRSLRNRVLAVVLQSI
QFTSE

Sequence of entity 5 (N), FASTA

>6QLE_5 Inner kinetochore subunit CHL4 (chains N)
MSNELRLEDNYVPTSDTLVVFKQLMKLPVTVLYDLTLSWFAKFGGSFDGDIYLLTETLDL
LIEKGVRRNVIVNRILYVYWPDGLNVFQLAEIDCHLMISKPEKFKWLPSKALRGDGKPYV
VKLQPAKFIENLQTDLAKIYHCHVYMFKHPSLPVLITRIQLFDSNNLFLSTPNIGSINKE
SLYNKLDKFQGKPLISRRPYYVAFPLNSPIIFHSVDKDIYARLVLQSISRTISERETIIF
KPVQKIPVKSIHNIMTLLGPSRFAESMGPWECYASANFERSPLHDYKKHQGLTGKKVMVR
EFDDSFLNDDENFYGKEEPEIRRLRLEKNMIKFKGSANGVMDQKYNDLKEFNEHVHNIRN
GKKNEDSGEPVYISRYSSLVPIEKVGFTLKNEINSRIITIKLKFNGNDIFGGLHELCDKN
LINIDKVPGWLAGENGSFSGTIMNGDFQREQVAKGGLL

Sequence of entity 6 (O), FASTA

>6QLE_6 Inner kinetochore subunit MCM21 (chains O)
MSRIDDLQQDIESLLSEINSLEESREKLKAKIKDKRKNEESANPIVQEFEDLFDQFPQLN
NFLFNEHPELEETDDKDISRAQADIPATPIPYEPKKRAKLENEEILPEQEWVLKTQPMVQ
HQMFDPGVADLLDTDILTSPSKRKRKLKIDDISTSDRSELEDYIVLENVYRMFGITFFPL
VDPIDLKIKDASGEIFVDREMLGIRLEVFSERTSQFEKPHYVLLKKRIKSNSWFLFKHTI
PSFIDVQGIFDDTNGGLVISHDDAYLFAKRVFLQLVEVQKRRQIFKDLEAKKIIHDLDLD
LESSMVSFFVKDIKVELFVKQNEIVSCSILDDIHDFSQNNKSKWEIALLGSLDDLELKLN
HSFATIFK

Sequence of entity 7 (P), FASTA

>6QLE_7 Inner kinetochore subunit CTF19 (chains P)
MDFTSDTTNSHDTSNSHLSLEDAVGTHHAGEADVNIDGDEKQQLSLLDDDQVRALKLQEE
KDALLTRRNTLLQEIQTYQNILMKENNSKTKNGDILQNDITQDFLNLISISSSNPNSAIS
DRKRVERINGLTNLQKELVTKYDTLPLLNMNLRLSYLRDHTYPHLQVSVQSRDRVHNDGI
EVLVVNYKFCRNTMNPFEIQFKMFYKFEDSTLLKWEILRISTNVRLKAKQLLATRNFQKC
LLSLYEFDKIKSKKTGIFQNLINLLKRKTRCYLMNNSDSLIVERVIREGRLTTIKLQINF
IITMPGERGKPRNCFLPMSKISIALWKGGERFNQIDLDEICYGLIKEYGVKTGLKEICNV
CLFPDMYAR

Sequence of entity 8 (Q), FASTA

>6QLE_8 Inner kinetochore subunit OKP1,Inner kinetochore subunit OKP1,Inner kinetochore subunit OKP1,Inner kinetochore subunit OKP1 (chains Q)
XXXXXXXXXXXXXXXSILRLLETNTVSALDSVFEKYEKEMNQMTHGDNNEVKRIYSKKER
LLEIILTKIKKKLRQAKFPSRISERDLDIEYIYSKRQFIQNRYSQELQNNERLEAILSRE
QNLLEETRKLCMNLKTNNKKRLTEKLIQKDLHPVLNKAMEYTYGLESTNGFMHPDGPVTF
RNDSHELNLMLNDPIKSTADVRLDKEEVLSLLPSLKEYTKKSKELKETMGQMISDSHEEE
IKEVFVPHHESHQDKTEEDIH

Sequence of entity 9 (U), FASTA

>6QLE_9 Inner kinetochore subunit AME1,Inner kinetochore subunit AME1,Inner kinetochore subunit AME1,Inner kinetochore subunit AME1 (chains U)
XXXXXXXXXXXXXXXXXXXXXXXXXXXFRKLLYKLDLRLFQTISDQMTRDLKDILDINVS
NNELCYQLKQVLARKEDLNQQIISVRNEIQELKAGKDWHDLQNEQAKLNDKVKLNKRLND
LTSTLLGKYEGDRKIMSQDSEDDSIRDDSNILDIAHFVDLMDPYNGLLKKINKINENLSN
ELQPSL

Sequence of entity 10 (Y), FASTA

>6QLE_10 Inner kinetochore subunit NKP1 (chains Y)
MTDTYNSISNFIENELTALLSSDDYLMDDLAGELPNEVCRLLKAQVIEKRKDAMSRGKQD
LLSKEIYDNESELRASQSQQIMELVGDIPKYSLGSELRNRVEGEPQSTSIERLIEDVLKL
PQMEVADEEEVEVENDLKVLSEYSNLRKDLILKCQALQIGESKLSDILSQTNSINSLTTS
IKEASEDDDISEYFATYNGKLVVALEEMKLLLEEAVKTFGNSPEKREKIKKILSELKK

Sequence of entity 11 (Z), FASTA

>6QLE_11 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 Q12262 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YPC 2.9 Å, Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae…
6WUC 3.23 Å, The yeast Ctf3 complex with Cnn1-Wip1
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
7L7Q 3.7 Å, Ctf3c with Ulp2-KIM
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
6OUA 4.18 Å, Cryo-EM structure of the yeast Ctf3 complex
10JC 6.5 Å, CCAN dimer purified from budding yeast

Browse structure collections

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