6gys

Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Centromere DNA-binding protein complex CBF3 subunit C

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Centromere DNA-binding protein complex CBF3 subunit B × 4 （P40969） Suppressor of kinetochore protein 1 × 2 （P52286） Centromere DNA-binding protein complex CBF3 subunit A × 2 （P32504） DNA (52-MER) × 1 DNA (52-MER) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBF3C_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–478； UniProt 1–478 Author chain H； PDBConstruct 1–478； UniProt 1–478

Centromere DNA-binding protein complex CBF3 subunit B

Saccharomyces cerevisiae

UniProt P40969

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Centromere DNA-binding protein complex CBF3 subunit C × 2 （P35203） Suppressor of kinetochore protein 1 × 2 （P52286） Centromere DNA-binding protein complex CBF3 subunit A × 2 （P32504） DNA (52-MER) × 1 DNA (52-MER) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBF3B_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–608； UniProt 1–608 Author chain C； PDBConstruct 1–608； UniProt 1–608 Author chain I； PDBConstruct 1–608； UniProt 1–608 Author chain J； PDBConstruct 1–608； UniProt 1–608

Suppressor of kinetochore protein 1

Saccharomyces cerevisiae

UniProt P52286

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Centromere DNA-binding protein complex CBF3 subunit C × 2 （P35203） Centromere DNA-binding protein complex CBF3 subunit B × 4 （P40969） Centromere DNA-binding protein complex CBF3 subunit A × 2 （P32504） DNA (52-MER) × 1 DNA (52-MER) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKP1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–194； UniProt 1–194 Author chain K； PDBConstruct 1–194； UniProt 1–194

Centromere DNA-binding protein complex CBF3 subunit A

Saccharomyces cerevisiae

UniProt P32504

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Centromere DNA-binding protein complex CBF3 subunit C × 2 （P35203） Centromere DNA-binding protein complex CBF3 subunit B × 4 （P40969） Suppressor of kinetochore protein 1 × 2 （P52286） DNA (52-MER) × 1 DNA (52-MER) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBF3A_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–956； UniProt 1–956 Author chain L； PDBConstruct 1–956； UniProt 1–956

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6gys
Deposition date deposition_date	2018-07-01
Structure title title	Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore
Keywords keywords	Complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6gys__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6gys__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6gys__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	76.63 Å
Rg (electron density)	77.92 Å
Total Rg	77.81 Å
Atom count	38890
Residues	4545
Excluded volume	690740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6gys__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit C
Molecular weight formula_weight	56416.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	38890

MPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSKKLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEWTYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQLVDKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASKRSHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKTISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLTMKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEINQITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

Entity 2 Entity 2 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit B
Molecular weight formula_weight	71439.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,I,J

MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLAEIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLIYYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSEYNISDILS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

Entity 3 Entity 3 polymer

Description description	Suppressor of kinetochore protein 1
Molecular weight formula_weight	22357.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,K

MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSKDNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

Entity 4 Entity 4 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit A
Molecular weight formula_weight	112066.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,L

MRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQIIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIATLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQVLCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSLKLGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSVSKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFNKCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTNAKKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFFPNHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQLTFASSHNPDTHPTQKQESEGPLQMSQLDTTQLNELLKQQSFEYVQFQTLSNFQILLSVFNKIFEKLEMKKSSRGYILHQLNLFKITLDERIKKSKIDDADKFIRDNQPIKKEENIVNEDGPNTSRRTKRPKQIRLLSIADSSDESSTEDSNVFKKDGESIEDGAYGENEDENDSEMQEQLKSMINELINSKISTFLRDQMDQFELKINALLDKILEEKVTRIIEQKLGSHTGKFSTLKRPQLYMTEEHNVGFDMEVPKKLRTSGKYAETVKDNDDHQAMSTTASPSPEQDQEAKSYTDEQEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGNKSWRANCEALYKERKSIVEFYIYLVNHESLDRYKAVDICEKLRDQNEGSFSRLAKFLRKWRHDHQNSFDGLLVYLSN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

Entity 5 Entity 5 polymer

Description description	DNA (52-MER)
Molecular weight formula_weight	16168.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TTAAAATATTAGTGTATTTGATTTCCGAAAGTTAAAAAAGAAATAGTAAGAA

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

Entity 6 Entity 6 polymer

Description description	DNA (52-MER)
Molecular weight formula_weight	15856.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

TTCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTAATATTTTAA

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	man
Copy count entity_count	8

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	unidentified baculovirus

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	4.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	22668

Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

1. Protein Identity and Related Structures Protein Identity & Related Structures

Centromere DNA-binding protein complex CBF3 subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Centromere DNA-binding protein complex CBF3 subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Suppressor of kinetochore protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Centromere DNA-binding protein complex CBF3 subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6gys__assembly_1__model_1

6gys__assembly_1__model_1 | I(q)

6gys__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Source Source

7. Citations (1)