6YPC: Inner kinetochore subunit MCM22

Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms. Determined by X-ray diffraction at 2.9 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 5
Atoms: 4,341
Mol. weight: 99.17 kDa
Released: 16 Sept 2020

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

Secondary structure: helices and β-sheets

6YPC contains 34 α-helices and 5 β-strands across 5 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	151-171	21

Chain I: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
α-helix	21-38	18
β-strand	40	1	2
α-helix	42-54	13
α-helix	60-70	11
β-strand	73	1	2
α-helix	77-78	2
α-helix	79-86	8
α-helix	104-116	13
α-helix	118-120	3
α-helix	121-125	5
α-helix	126-140	15
α-helix	143-145	3
α-helix	146-156	11
α-helix	165-176	12
α-helix	183-198	16
α-helix	202-210	9
α-helix	217-222	6
α-helix	228-240	13

Chain K: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	139-155	17
α-helix	156-160	5
α-helix	171-186	16
β-strand	193	1	1
α-helix	194-196	3
α-helix	202-211	10
β-strand	214-217	4	1
β-strand	227-230	4	1
α-helix	231-232	2

Chain T: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	273-274	2
α-helix	275-281	7
α-helix	283-288	6
α-helix	295-315	21
α-helix	323-330	8
α-helix	337-347	11
α-helix	350-359	10

Chain W: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-14	12
α-helix	37-67	31
α-helix	75-88	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Inner kinetochore subunit MCM22	K	protein	110	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P47167 (AlphaFold model)
Inner kinetochore subunit MCM16	H	protein	46	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12262 (AlphaFold model)
Inner kinetochore subunit CNN1	T	protein	367	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P43618 (AlphaFold model)
Inner kinetochore subunit WIP1	W	protein	89	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q2V2P8 (AlphaFold model)
Inner kinetochore subunit CTF3	I	protein	251	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12748

Sequence of entity 1 (K), FASTA

>6YPC_1 Inner kinetochore subunit MCM22 (chains K)
MKKQDHAHIRTRKARNKELWDSLADFLKGYLVPNLDDNDESIDSLTNEVMLLMKRLIEHD
LNLTLNDFSSKTIPIYRLLLRANIITVIEGSTNPGTKYIKLIDFNETSLT

Sequence of entity 2 (H), FASTA

>6YPC_2 Inner kinetochore subunit MCM16 (chains H)
MKPTIPPDDSDTAGKQVEVEKENETIQELMIALQIHSGYTNISYTI

Sequence of entity 3 (T), FASTA

>6YPC_3 Inner kinetochore subunit CNN1 (chains T)
MSTPRKAAGNNENTEVSEIRTPFRERALEEQRLKDEVLIRNTPGYRKLLSASTKSHDILN
KDPNEVRSFLQDLSQVLARKSQGNDTTTNKTQARNLIDELAYEESQPEENELLRSRSEKL
TDNNIGNETQPDYTSLSQTVFAKLQERDKGLKSRKIDPIIIQDVPTTGHEDELTVHSPDK
ANSISMEVLRTSPSIGMDQVDEPPVRDPVPISITQQEEPLSEDLPSDDKEETEEAENEDY
SFENTSDENLDDIGNDPIRLNVPAVRRSSIKPLQIMDLKHLTRQFLNENRIILPKQTWST
IQEESLNIMDFLKQKIGTLQKQELVDSFIDMGIINNVDDMFELAHELLPLELQSRIESYL
FENLYFQ

Sequence of entity 4 (W), FASTA

>6YPC_4 Inner kinetochore subunit WIP1 (chains W)
MDTEALANYLLRQLSLDAEENKLEDLLQRQNEDQESSQEYNKKLLLACGFQAILRKILLD
ARTRATAEGLREVYPYHIEAATQAFLDSQ

Sequence of entity 5 (I), FASTA

>6YPC_5 Inner kinetochore subunit CTF3 (chains I)
MSLILDDIILSLTNANERTPPQALKTTLSLLYEKSKQYGLSSPQLQALVRLLCETSIIDT
VTKVYIVENCFLPDGYLTKELLLEIINHLGTPTVFSRYRIQTPPVLQSALCKWLVHVYFL
FPVHSEREHNISSSIWLHLWQFSFLQKWITPLVIWQATTPVDVKPWKLSIIKRCAMHPGY
RDAPGSATLILQRFQCLVGASSQITESIITINCNRKTLKSHRNLKLDAHFLSILKRILSR
AHPANENLYFQ

Primary citation

Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex. Zhang, Z., Bellini, D., Barford, D. Nucleic Acids Res (2020) 48:11172-11184. DOI 10.1093/nar/gkaa772 · PubMed

Other PDB entries of the same protein (UniProt P47167 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
6QLE 3.55 Å, Structure of inner kinetochore CCAN complex
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

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