6GSA: PDB entry 6GSA

Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10. Determined by electron microscopy at 4.2 Å resolution. Released 1 Aug 2018.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 16,272
Mol. weight: 286.53 kDa
Released: 1 Aug 2018

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

Secondary structure: helices and β-sheets

6GSA contains 117 α-helices and 46 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: 35 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	58-68	11
α-helix	69-75	7
α-helix	76-78	3
β-strand	89	1	1
α-helix	90	1
α-helix	96-104	9
α-helix	108-120	13
α-helix	123-126	4
α-helix	133-135	3
α-helix	136-146	11
β-strand	153	1	2
α-helix	154-172	19
α-helix	176-182	7
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	250-265	16
α-helix	280-301	22
β-strand	315-316	2	3
α-helix	317	1
β-strand	332-333	2	3
α-helix	341-355	15
α-helix	364-366	3
α-helix	367-385	19
α-helix	395-417	23
α-helix	418-422	5
α-helix	427-443	17
α-helix	444-446	3
α-helix	451-455	5
α-helix	458-476	19
α-helix	480-494	15
α-helix	498-500	3
α-helix	501-523	23
β-strand	527-528	2	4
β-strand	533-534	2	4
α-helix	536-550	15
α-helix	555-562	8
α-helix	589-600	12
α-helix	603-606	4

Chain B: 29 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	57-70	14
α-helix	71-76	6
α-helix	77-78	2
β-strand	89	1	2
α-helix	96-104	9
α-helix	108-121	14
α-helix	123-126	4
α-helix	137-146	10
β-strand	153	1	1
α-helix	154-172	19
α-helix	176-182	7
α-helix	186-192	7
α-helix	200-204	5
α-helix	205-222	18
α-helix	232-240	9
α-helix	245-248	4
α-helix	250-265	16
α-helix	280-301	22
α-helix	340-356	17
α-helix	367-386	20
α-helix	394-417	24
α-helix	418-422	5
α-helix	428-443	16
α-helix	451-455	5
α-helix	457-476	20
α-helix	480-494	15
α-helix	502-523	22
β-strand	527-528	2	5
β-strand	533-534	2	5
α-helix	536-551	16
α-helix	555-562	8
α-helix	589-600	12
α-helix	604-606	3

Chain C: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	6
β-strand	15-19	5	6
α-helix	20-23	4
α-helix	29-32	4
β-strand	76-78	3	6
α-helix	84-96	13
α-helix	108-112	5
α-helix	118-123	6
α-helix	128-140	13
α-helix	144-159	16
α-helix	161-162	2
α-helix	178-187	10

Chain D: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	14-22	9
α-helix	98-110	13
β-strand	118-123	6	7
β-strand	126-132	7	7
β-strand	138-142	5	7
α-helix	144-155	12
α-helix	177-189	13
β-strand	198-200	3	8
α-helix	258-266	9
β-strand	275-278	4	8
α-helix	281-287	7
β-strand	311-314	4	8
β-strand	319	1	9
β-strand	327	1	10
β-strand	336-339	4	8
β-strand	344	1	9
β-strand	346	1	11
β-strand	351	1	10
β-strand	358-361	4	8
β-strand	367	1	12
β-strand	368	1	11
α-helix	372-380	9
α-helix	384-388	5
β-strand	391-392	2	13
β-strand	409-411	3	14
β-strand	412-413	2	13
α-helix	420-431	12
β-strand	439-442	4	8
β-strand	448	1	12
β-strand	452-455	4	14
α-helix	456-458	3
β-strand	465-466	2	8
β-strand	474-478	5	14

Chain E: 33 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	45-58	14
α-helix	82-89	8
α-helix	90-94	5
α-helix	108-138	31
α-helix	148-167	20
α-helix	184-193	10
α-helix	208-224	17
α-helix	228-231	4
β-strand	235	1	15
α-helix	236-238	3
β-strand	239-241	3	16
β-strand	249-255	7	16
β-strand	266-272	7	16
α-helix	278-280	3
α-helix	282-295	14
β-strand	297	1	17
β-strand	301	1	17
α-helix	309-311	3
α-helix	318-320	3
β-strand	322	1	15
α-helix	332-334	3
α-helix	335-348	14
α-helix	356-359	4
α-helix	361-362	2
β-strand	368-370	3	16
α-helix	371-377	7
α-helix	380-383	4
α-helix	390-392	3
α-helix	396-398	3
α-helix	401-407	7
α-helix	426-428	3
α-helix	429-432	4
α-helix	438-444	7
α-helix	447-449	3
α-helix	452-478	27
α-helix	483-486	4
α-helix	488-491	4
α-helix	493-503	11
α-helix	504-506	3
β-strand	511	1	18
α-helix	521-524	4
β-strand	526	1	18
α-helix	527-531	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit B	A, B	protein	584	Saccharomyces cerevisiae	P40969 (AlphaFold model)
Suppressor of kinetochore protein 1	C	protein	197	Saccharomyces cerevisiae	P52286 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit C	D	protein	519	Saccharomyces cerevisiae	P35203 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit A	E	protein	562	Saccharomyces cerevisiae	P32504 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GSA_1 Centromere DNA-binding protein complex CBF3 subunit B (chains A, B)
MGGSSHHHHHHSSGLVPRGSHMKLITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRD
LTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYW
DRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLAEIFSVYPLHEYLGSNKRLNWEDGM
QLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTF
KNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAA
YLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKV
DSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLIYYDTADSLLKVIHYSKVIISLIVN
NFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKL
DKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGS
LVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSEYNISDILS

Sequence of entity 2 (C), FASTA

>6GSA_2 Suppressor of kinetochore protein 1 (chains C)
MGVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKS
KDNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSW
DREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPE
EEAAIRRENEWAEDRGS

Sequence of entity 3 (D), FASTA

>6GSA_3 Centromere DNA-binding protein complex CBF3 subunit C (chains D)
MGPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRS
KKLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALE
WTYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQL
VDKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASK
RSHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGK
TISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSL
TMKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEIN
QITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVIG
SRSGSENLYFQGSKRRWKKNFIAVSAANRFKKISSSGAL

Sequence of entity 4 (E), FASTA

>6GSA_4 Centromere DNA-binding protein complex CBF3 subunit A (chains E)
MGRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLN
QIIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKI
ATLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQ
VLCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSL
KLGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPS
VSKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYF
NKCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTN
AKKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFF
PNHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPS
QLTFASSHNPDTHPWSHPQFEK

Primary citation

Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. Zhang, W., Lukoynova, N., Miah, S. et al. Cell Rep (2018) 24:744-754. DOI 10.1016/j.celrep.2018.06.068 · 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
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
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

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