6GYU: PDB entry 6GYU

Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore. Determined by electron microscopy at 3.0 Å resolution. Released 5 Dec 2018.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 5
Atoms: 18,159
Mol. weight: 328.81 kDa
Ligands: ZN
Released: 5 Dec 2018

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

Secondary structure: helices and β-sheets

6GYU contains 128 α-helices and 56 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 A: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	14-23	10
α-helix	33-35	3
β-strand	44-46	3	6
α-helix	59-65	7
α-helix	71-74	4
α-helix	75-77	3
α-helix	82-93	12
α-helix	98-108	11
β-strand	119-120	2	7
β-strand	129-130	2	7
β-strand	131-132	2	8
β-strand	138-140	3	8
α-helix	144-147	4
α-helix	148-152	5
α-helix	153-155	3
β-strand	168-169	2	7
α-helix	177-189	13
β-strand	196-198	3	7
α-helix	258-265	8
β-strand	276-278	3	9
α-helix	284-287	4
β-strand	311-314	4	9
β-strand	319	1	10
β-strand	326	1	11
β-strand	336-339	4	9
β-strand	344-345	2	10
α-helix	347-349	3
β-strand	350	1	11
β-strand	358-361	4	9
β-strand	366-367	2	10
α-helix	372-379	8
α-helix	384-386	3
α-helix	387-391	5
β-strand	392	1	12
β-strand	411-412	2	13
β-strand	413	1	12
α-helix	424-434	11
β-strand	439	1	9
β-strand	442	1	9
β-strand	448	1	10
α-helix	451	1
β-strand	452-454	3	13
α-helix	456-459	4
α-helix	460-462	3
β-strand	475-477	3	13

Chain B: 36 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
α-helix	15-20	6
α-helix	40-43	4
β-strand	44	1	1
β-strand	46	1	1
α-helix	58-68	11
α-helix	69-76	8
α-helix	77-78	2
β-strand	89	1	2
α-helix	95-105	11
α-helix	108-121	14
α-helix	123-129	7
α-helix	133-135	3
α-helix	137-145	9
β-strand	152-153	2	3
α-helix	154-173	20
α-helix	176-182	7
α-helix	186-192	7
α-helix	200-202	3
α-helix	205-223	19
α-helix	231-240	10
α-helix	245-248	4
α-helix	252-265	14
α-helix	280-301	22
β-strand	305	1	4
β-strand	308	1	4
α-helix	344-347	4
α-helix	350-356	7
α-helix	364-366	3
α-helix	367-385	19
α-helix	395-421	27
α-helix	427-442	16
α-helix	443-446	4
α-helix	451-455	5
α-helix	457-476	20
α-helix	481-494	14
α-helix	502-521	20
α-helix	525-526	2
β-strand	527-528	2	5
β-strand	533-534	2	5
α-helix	536-551	16
α-helix	555-561	7
α-helix	589-600	12
α-helix	603-606	4

Chain C: 33 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	14
α-helix	57-68	12
α-helix	69-74	6
β-strand	89-90	2	3
α-helix	95-105	11
α-helix	108-121	14
α-helix	123-126	4
α-helix	134-136	3
α-helix	137-145	9
β-strand	153	1	2
α-helix	154-172	19
α-helix	176-182	7
α-helix	186-192	7
α-helix	205-223	19
α-helix	231-240	10
α-helix	245-248	4
α-helix	250-265	16
α-helix	274-275	2
α-helix	280-302	23
β-strand	305	1	15
β-strand	308	1	15
α-helix	313-315	3
α-helix	317-318	2
α-helix	342-355	14
α-helix	356-358	3
α-helix	364-366	3
α-helix	367-385	19
α-helix	394-421	28
α-helix	428-442	15
α-helix	444-447	4
α-helix	451-455	5
α-helix	458-476	19
α-helix	480-494	15
α-helix	502-523	22
β-strand	527-528	2	14
α-helix	536-551	16
α-helix	555-562	8
α-helix	589-600	12
α-helix	603-605	3

Chain D: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	16
β-strand	15-19	5	16
α-helix	23-25	3
α-helix	27-32	6
β-strand	75-78	4	16
α-helix	84-96	13
α-helix	109-112	4
α-helix	114-117	4
α-helix	118-123	6
α-helix	128-140	13
α-helix	146-149	4
α-helix	152-158	7
α-helix	164-168	5
α-helix	178-187	10

Chain E: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
α-helix	39-58	20
β-strand	72-74	3	6
α-helix	75-77	3
β-strand	80	1	17
α-helix	82-88	7
α-helix	89-94	6
α-helix	108-137	30
β-strand	144	1	17
α-helix	148-169	22
α-helix	177-181	5
α-helix	184-192	9
α-helix	208-222	15
α-helix	228-232	5
β-strand	235	1	18
β-strand	239-241	3	19
β-strand	249-251	3	19
β-strand	252-256	5	20
β-strand	265-269	5	20
β-strand	272	1	19
α-helix	273-275	3
α-helix	282-294	13
β-strand	296	1	21
β-strand	302	1	21
β-strand	322	1	18
α-helix	335-348	14
β-strand	368	1	20
α-helix	371-376	6
α-helix	380-382	3
α-helix	396-398	3
α-helix	401-407	7
α-helix	426-428	3
α-helix	429-432	4
α-helix	438-443	6
α-helix	452-478	27
α-helix	483-485	3
α-helix	493-503	11
α-helix	504-506	3
β-strand	511	1	22
β-strand	526	1	22
α-helix	527-532	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit B	B	protein	608	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40969 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit C	A	protein	478	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P35203 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit B	C	protein	564	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40969 (AlphaFold model)
Suppressor of kinetochore protein 1	D	protein	194	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P52286 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit A	E	protein	956	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32504 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6GYU_1 Centromere DNA-binding protein complex CBF3 subunit B (chains B)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPD
LLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAME
NLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLA
EIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLIL
ATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCD
YLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLN
KSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLI
YYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESA
AVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKI
LQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSE
YNISDILS

Sequence of entity 2 (A), FASTA

>6GYU_2 Centromere DNA-binding protein complex CBF3 subunit C (chains A)
MPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSK
KLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEW
TYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQLV
DKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASKR
SHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKT
ISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLT
MKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEINQ
ITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVI

Sequence of entity 3 (C), FASTA

>6GYU_3 Centromere DNA-binding protein complex CBF3 subunit B (chains C)
MFNRITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMN
YLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIW
SVFTMCIYYMPVEKLAEIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCD
FMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESI
AKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVL
YWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIAL
FQISTVSWKLFKMYLIYYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTIT
RVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKV
QLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENN
TEPSDFRTIVEEFQSEYNISDILS

Sequence of entity 4 (D), FASTA

>6GYU_4 Suppressor of kinetochore protein 1 (chains D)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR

Sequence of entity 5 (E), FASTA

>6GYU_5 Centromere DNA-binding protein complex CBF3 subunit A (chains E)
MRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQ
IIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIA
TLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQV
LCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSLK
LGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSV
SKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFN
KCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTNA
KKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFFP
NHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQ
LTFASSHNPDTHPTQKQESEGPLQMSQLDTTQLNELLKQQSFEYVQFQTLSNFQILLSVF
NKIFEKLEMKKSSRGYILHQLNLFKITLDERIKKSKIDDADKFIRDNQPIKKEENIVNED
GPNTSRRTKRPKQIRLLSIADSSDESSTEDSNVFKKDGESIEDGAYGENEDENDSEMQEQ
LKSMINELINSKISTFLRDQMDQFELKINALLDKILEEKVTRIIEQKLGSHTGKFSTLKR
PQLYMTEEHNVGFDMEVPKKLRTSGKYAETVKDNDDHQAMSTTASPSPEQDQEAKSYTDE
QEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGNKSWRANCEALYKERKSIVEFY
IYLVNHESLDRYKAVDICEKLRDQNEGSFSRLAKFLRKWRHDHQNSFDGLLVYLSN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Architecture of the CBF3-centromere complex of the budding yeast kinetochore. Yan, K., Zhang, Z., Yang, J. et al. Nat Struct Mol Biol (2018) 25:1103-1110. DOI 10.1038/s41594-018-0154-1 · 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
10EH 3.5 Å, De novo assembled CBF3-CEN complex
6F07 3.6 Å, CBF3 Core 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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