6GYP: PDB entry 6GYP

Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore. Determined by electron microscopy at 3.6 Å resolution. Released 5 Dec 2018.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 5
Atoms: 17,811
Mol. weight: 329.69 kDa
Ligands: ARG, ASN, PHE, MET
Released: 5 Dec 2018

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

Secondary structure: helices and β-sheets

6GYP contains 124 α-helices and 44 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, 22 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	14-21	8
α-helix	32-35	4
β-strand	46	1	5
α-helix	57-65	9
α-helix	75-77	3
α-helix	84-93	10
α-helix	94-96	3
α-helix	98-108	11
β-strand	119-120	2	6
β-strand	129-130	2	6
β-strand	131-132	2	7
β-strand	138-140	3	7
α-helix	144-147	4
α-helix	148-152	5
α-helix	153-155	3
β-strand	168-169	2	6
α-helix	177-189	13
β-strand	196-198	3	6
α-helix	258-264	7
α-helix	267-269	3
β-strand	276-278	3	8
α-helix	281-287	7
β-strand	311-314	4	8
β-strand	319	1	9
β-strand	326	1	10
β-strand	336-339	4	8
β-strand	344-345	2	9
α-helix	347-349	3
β-strand	350	1	10
β-strand	360-361	2	8
β-strand	366-367	2	9
α-helix	372-379	8
α-helix	384-390	7
β-strand	411-412	2	11
α-helix	424-434	11
β-strand	442	1	8
β-strand	448	1	9
α-helix	451	1
β-strand	452-454	3	11
α-helix	456-459	4
α-helix	460-462	3
β-strand	466	1	8
β-strand	475-477	3	11

Chain B: 34 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	59-68	10
α-helix	69-74	6
α-helix	75-78	4
β-strand	89-90	2	1
α-helix	95-104	10
α-helix	108-121	14
α-helix	126-129	4
α-helix	133-135	3
α-helix	137-145	9
β-strand	153	1	2
α-helix	154-172	19
α-helix	176-180	5
α-helix	186-192	7
α-helix	200-202	3
α-helix	205-221	17
α-helix	231-240	10
α-helix	245-248	4
α-helix	252-264	13
α-helix	274-275	2
α-helix	280-301	22
β-strand	305	1	3
β-strand	308	1	3
α-helix	344-356	13
α-helix	364-366	3
α-helix	367-384	18
α-helix	395-421	27
α-helix	427-443	17
α-helix	444-446	3
α-helix	451-455	5
α-helix	457-476	20
α-helix	481-493	13
α-helix	498-500	3
α-helix	502-523	22
α-helix	525-526	2
β-strand	527-528	2	4
β-strand	533-534	2	4
α-helix	536-551	16
α-helix	555-559	5
α-helix	589-600	12
α-helix	603-606	4

Chain C: 32 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	12
α-helix	57-68	12
α-helix	69-74	6
β-strand	89	1	2
α-helix	94-105	12
α-helix	108-121	14
α-helix	126-129	4
α-helix	133-135	3
α-helix	137-143	7
α-helix	146-148	3
β-strand	152-153	2	1
α-helix	154-172	19
α-helix	176-182	7
α-helix	186-192	7
α-helix	205-222	18
α-helix	231-240	10
α-helix	245-248	4
α-helix	250-265	16
α-helix	280-301	22
α-helix	313-315	3
α-helix	342-356	15
α-helix	364-366	3
α-helix	367-384	18
α-helix	394-421	28
α-helix	428-442	15
α-helix	443-447	5
α-helix	451-455	5
α-helix	458-476	19
α-helix	480-493	14
α-helix	498-500	3
α-helix	502-523	22
β-strand	527-528	2	12
α-helix	536-551	16
α-helix	555-561	7
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	13
β-strand	15-19	5	13
α-helix	20-23	4
α-helix	27-32	6
β-strand	75-78	4	13
α-helix	84-96	13
α-helix	109-112	4
α-helix	114-117	4
α-helix	118-121	4
α-helix	128-140	13
α-helix	144-149	6
α-helix	152-158	7
α-helix	164-168	5
α-helix	178-187	10

Chain E: 25 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
α-helix	39-58	20
β-strand	72	1	5
α-helix	82-88	7
α-helix	89-94	6
α-helix	108-138	31
α-helix	148-169	22
α-helix	177-181	5
α-helix	184-191	8
α-helix	208-221	14
α-helix	228-232	5
β-strand	239-240	2	14
β-strand	250-253	4	14
β-strand	266-270	5	14
α-helix	282-294	13
β-strand	296	1	15
β-strand	302	1	15
α-helix	335-348	14
α-helix	361-362	2
α-helix	366-367	2
β-strand	368-370	3	14
α-helix	371-376	6
α-helix	380-383	4
α-helix	401-407	7
α-helix	430-434	5
α-helix	437-443	7
α-helix	452-478	27
α-helix	483-485	3
α-helix	488-490	3
α-helix	493-502	10
α-helix	503-505	3
β-strand	511	1	16
β-strand	526	1	16
α-helix	527-531	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit B	B	protein	608	Saccharomyces cerevisiae S288C	P40969 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit C	A	protein	478	Saccharomyces cerevisiae S288C	P35203 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit B	C	protein	564	Saccharomyces cerevisiae S288C	P40969 (AlphaFold model)
Suppressor of kinetochore protein 1	D	protein	194	Saccharomyces cerevisiae S288C	P52286 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit A	E	protein	956	Saccharomyces cerevisiae S288C	P32504 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6GYP_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

>6GYP_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

>6GYP_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

>6GYP_4 Suppressor of kinetochore protein 1 (chains D)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR

Sequence of entity 5 (E), FASTA

>6GYP_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
ARG	Arginine	C6 H15 N4 O2	1
ASN	Asparagine	C4 H8 N2 O3	1
PHE	Phenylalanine	C9 H11 N O2	1
MET	Methionine	C5 H11 N O2 S	1
GLN	Glutamine	C5 H10 N2 O3	1
THR	Threonine	C4 H9 N O3	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
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
6F07 3.6 Å, CBF3 Core Complex
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

About this viewer

MolViewer shows 6GYP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.