7K79: CBF3

CBF3. Determined by electron microscopy at 4.0 Å resolution. Released 31 Mar 2021.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 13,272
Mol. weight: 228.53 kDa
Released: 31 Mar 2021

Explore 7K79 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K79 contains 84 α-helices and 33 β-strands across 4 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 K: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	14-23	10
α-helix	62-65	4
α-helix	70-73	4
α-helix	86-90	5
α-helix	98-106	9
β-strand	118	1	1
β-strand	131-132	2	1
β-strand	138-140	3	1
α-helix	144-150	7
β-strand	172	1	2
α-helix	177-184	8
α-helix	193-195	3
β-strand	199-201	3	2
α-helix	258-265	8
β-strand	275-278	4	2
α-helix	281-287	7
α-helix	305-307	3
β-strand	311-314	4	2
β-strand	319	1	3
β-strand	326	1	4
β-strand	336-339	4	2
β-strand	342	1	5
β-strand	344	1	3
β-strand	345	1	6
α-helix	347-349	3
β-strand	350	1	4
β-strand	358-360	3	2
β-strand	361	1	7
β-strand	364	1	5
β-strand	367	1	6
α-helix	369-371	3
α-helix	373-379	7
α-helix	384-389	6
α-helix	399-401	3
β-strand	410-412	3	8
α-helix	424-433	10
β-strand	439	1	2
β-strand	442	1	7
β-strand	445	1	5
β-strand	448	1	6
α-helix	451-452	2
β-strand	453-454	2	8
α-helix	456-459	4
β-strand	466	1	7
β-strand	475-477	3	8

Chain L: 29 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	59-71	13
α-helix	89-90	2
α-helix	98-105	8
α-helix	108-121	14
α-helix	134-144	11
α-helix	154-172	19
α-helix	176-180	5
α-helix	186-189	4
α-helix	200-202	3
α-helix	204-223	20
α-helix	231-240	10
α-helix	245-248	4
α-helix	250-265	16
α-helix	274-275	2
α-helix	280-301	22
α-helix	344-356	13
α-helix	357-359	3
α-helix	367-383	17
α-helix	388-389	2
α-helix	394-417	24
α-helix	418-422	5
α-helix	429-444	16
α-helix	452-455	4
α-helix	459-476	18
α-helix	482-493	12
α-helix	502-521	20
β-strand	527-528	2	9
β-strand	533-534	2	9
α-helix	537-551	15
α-helix	555-561	7
α-helix	591-600	10

Chain N: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	11
β-strand	15	1	11
α-helix	23-25	3
α-helix	27-30	4
β-strand	78	1	11
α-helix	84-96	13
α-helix	122-124	3
α-helix	129-141	13
α-helix	144-156	13
α-helix	178-186	9

Chain O: 29 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	57-72	16
α-helix	99-102	4
α-helix	108-117	10
α-helix	126-128	3
α-helix	134-146	13
α-helix	155-170	16
α-helix	171-173	3
α-helix	176-181	6
α-helix	204-223	20
α-helix	231-233	3
α-helix	234-240	7
α-helix	245-248	4
α-helix	250-265	16
α-helix	280-303	24
α-helix	341-343	3
α-helix	347-356	10
α-helix	364-366	3
α-helix	367-385	19
α-helix	394-421	28
α-helix	427-434	8
α-helix	436-444	9
α-helix	452-455	4
α-helix	459-474	16
α-helix	482-493	12
α-helix	498-500	3
α-helix	502-523	22
β-strand	527-528	2	10
β-strand	533-534	2	10
α-helix	536-551	16
α-helix	555-562	8
α-helix	603-605	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit C	K	protein	519	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P35203 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit B	L, O	protein	620	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40969 (AlphaFold model)
Suppressor of kinetochore protein 1	N	protein	194	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P52286 (AlphaFold model)

Sequence of entity 1 (K), FASTA

>7K79_1 Centromere DNA-binding protein complex CBF3 subunit C (chains K)
MGPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRS
KKLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALE
WTYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQL
VDKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASK
RSHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGK
TISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSL
TMKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEIN
QITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVIG
SRSGSENLYFQGSKRRWKKNFIAVSAANRFKKISSSGAL

Sequence of entity 2 (L, O), FASTA

>7K79_2 Centromere DNA-binding protein complex CBF3 subunit B (chains L, O)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPD
LLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAME
NLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLA
EIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLIL
ATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCD
YLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLN
KSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLI
YYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESA
AVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKI
LQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSE
YNISDILSGSGGSGENLYFQ

Sequence of entity 3 (N), FASTA

>7K79_3 Suppressor of kinetochore protein 1 (chains N)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR

Primary citation

Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation. Guan, R., Lian, T., Zhou, B.R. et al. Nat Commun (2021) 12:1763-1763. DOI 10.1038/s41467-021-21985-9 · PubMed

Other PDB entries of the same protein (UniProt P35203 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GYU 3.0 Å, Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore
10EH 3.5 Å, De novo assembled CBF3-CEN complex
6GYP 3.6 Å, Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore
6FE8 3.7 Å, Cryo-EM structure of the core Centromere Binding Factor 3 complex
8OW1 3.7 Å, Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome.
6GSA 4.2 Å, Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10
6GYS 4.4 Å, Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

Browse structure collections

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