6F07: CBF3 Core Complex

CBF3 Core Complex. Determined by electron microscopy at 3.6 Å resolution. Released 13 Dec 2017.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 10,149
Mol. weight: 167.76 kDa
Ligands: ZN
Released: 13 Dec 2017

Explore 6F07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F07 contains 74 α-helices and 9 β-strands across 3 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 A: 30 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	58-68	11
α-helix	69-76	8
β-strand	89	1	1
α-helix	90	1
α-helix	96-104	9
α-helix	108-121	14
α-helix	123-126	4
α-helix	136-145	10
α-helix	155-172	18
α-helix	176-182	7
α-helix	186-191	6
α-helix	200-204	5
α-helix	205-222	18
α-helix	232-240	9
α-helix	245-247	3
α-helix	250-265	16
α-helix	280-301	22
α-helix	339-356	18
α-helix	367-385	19
α-helix	394-421	28
α-helix	427-443	17
α-helix	444-446	3
α-helix	452-455	4
α-helix	457-476	20
α-helix	480-493	14
α-helix	498-500	3
α-helix	501-522	22
β-strand	527-528	2	2
β-strand	533-534	2	2
α-helix	536-551	16
α-helix	555-562	8
α-helix	589-600	12
α-helix	604-606	3

Chain B: 35 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
α-helix	15-19	5
α-helix	33-36	4
α-helix	39-43	5
β-strand	44	1	3
β-strand	46	1	3
α-helix	58-68	11
α-helix	69-74	6
α-helix	75-78	4
α-helix	89-90	2
α-helix	96-104	9
α-helix	108-121	14
α-helix	123-126	4
α-helix	134-145	12
β-strand	153	1	1
α-helix	154-172	19
α-helix	176-182	7
α-helix	186-191	6
α-helix	200-202	3
α-helix	204-222	19
α-helix	225-227	3
α-helix	231-240	10
α-helix	245-248	4
α-helix	250-265	16
α-helix	280-301	22
α-helix	342-356	15
α-helix	367-385	19
α-helix	394-421	28
α-helix	427-443	17
α-helix	452-455	4
α-helix	457-476	20
α-helix	480-493	14
α-helix	498-500	3
α-helix	501-522	22
α-helix	536-551	16
α-helix	555-562	8
α-helix	590-600	11
α-helix	603-605	3

Chain D: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	4
β-strand	15-18	4	4
α-helix	20-23	4
α-helix	27-33	7
β-strand	76-78	3	4
α-helix	84-96	13
α-helix	108-111	4
α-helix	115-117	3
α-helix	118-123	6
α-helix	128-141	14
α-helix	144-158	15
α-helix	178-186	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit B	A, B	protein	620	Saccharomyces cerevisiae	P40969 (AlphaFold model)
Suppressor of kinetochore protein 1	D	protein	194	Saccharomyces cerevisiae	P52286 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6F07_1 Centromere DNA-binding protein complex CBF3 subunit B (chains A, B)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPD
LLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAME
NLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLA
EIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLIL
ATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCD
YLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLN
KSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLI
YYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESA
AVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKI
LQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSE
YNISDILSGSGGSGENLYFQ

Sequence of entity 2 (D), FASTA

>6F07_2 Suppressor of kinetochore protein 1 (chains D)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural basis for assembly of the CBF3 kinetochore complex. Leber, V., Nans, A., Singleton, M.R. EMBO J (2018) 37:269-281. DOI 10.15252/embj.201798134 · PubMed

Other PDB entries of the same protein (UniProt P40969 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VEQ 2.49 Å, Insights into kinetochore-DNA interactions from the structure of Cep3p
2QUQ 2.8 Å, Crystal Structure of the Essential Inner Kinetochore Protein Cep3p
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.
7K79 4.0 Å, CBF3
6GSA 4.2 Å, Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10
7K7G 4.2 Å, nucleosome and Gal4 complex
6GYS 4.4 Å, Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

Browse structure collections

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