6GYS: PDB entry 6GYS
Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore. Determined by electron microscopy at 4.4 Å resolution. Released 5 Dec 2018.
- Method
- Electron microscopy
- Resolution
- 4.4 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 12
- Atoms
- 38,890
- Mol. weight
- 699.99 kDa
- Ligands
- ZN
- Released
- 5 Dec 2018
Explore 6GYS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6GYS contains 243 α-helices and 83 β-strands across 10 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: 20 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-11 | 6 | |
| α-helix | 14-22 | 9 | |
| α-helix | 57-65 | 9 | |
| α-helix | 67-70 | 4 | |
| α-helix | 74-77 | 4 | |
| α-helix | 81-91 | 11 | |
| α-helix | 94-96 | 3 | |
| α-helix | 98-109 | 12 | |
| β-strand | 118-120 | 3 | 1 |
| β-strand | 129-130 | 2 | 1 |
| β-strand | 131-132 | 2 | 2 |
| β-strand | 138-140 | 3 | 2 |
| α-helix | 144-147 | 4 | |
| α-helix | 148-152 | 5 | |
| α-helix | 160-163 | 4 | |
| β-strand | 168-169 | 2 | 1 |
| α-helix | 177-188 | 12 | |
| β-strand | 196-198 | 3 | 1 |
| α-helix | 258-266 | 9 | |
| α-helix | 267-269 | 3 | |
| β-strand | 276-278 | 3 | 3 |
| α-helix | 281-287 | 7 | |
| α-helix | 303-308 | 6 | |
| β-strand | 311-314 | 4 | 3 |
| β-strand | 319 | 1 | 4 |
| β-strand | 326 | 1 | 5 |
| β-strand | 336-339 | 4 | 3 |
| β-strand | 344-345 | 2 | 4 |
| β-strand | 350 | 1 | 5 |
| β-strand | 358-361 | 4 | 3 |
| β-strand | 366-367 | 2 | 4 |
| α-helix | 372-376 | 5 | |
| α-helix | 384-389 | 6 | |
| β-strand | 410-411 | 2 | 6 |
| α-helix | 424-434 | 11 | |
| β-strand | 439 | 1 | 3 |
| β-strand | 442 | 1 | 3 |
| β-strand | 448 | 1 | 4 |
| β-strand | 452-454 | 3 | 6 |
| α-helix | 456-459 | 4 | |
| β-strand | 466 | 1 | 3 |
| β-strand | 475-477 | 3 | 6 |
Chain B: 35 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| α-helix | 15-20 | 6 | |
| α-helix | 34-36 | 3 | |
| α-helix | 39-43 | 5 | |
| α-helix | 58-70 | 13 | |
| α-helix | 71-76 | 6 | |
| β-strand | 89 | 1 | 7 |
| α-helix | 96-105 | 10 | |
| α-helix | 108-121 | 14 | |
| α-helix | 122-124 | 3 | |
| α-helix | 126-129 | 4 | |
| α-helix | 133-145 | 13 | |
| α-helix | 146-148 | 3 | |
| α-helix | 154-173 | 20 | |
| α-helix | 176-180 | 5 | |
| α-helix | 186-192 | 7 | |
| α-helix | 200-202 | 3 | |
| α-helix | 204-223 | 20 | |
| α-helix | 231-241 | 11 | |
| α-helix | 245-248 | 4 | |
| α-helix | 250-265 | 16 | |
| α-helix | 280-302 | 23 | |
| α-helix | 343-356 | 14 | |
| α-helix | 364-366 | 3 | |
| α-helix | 367-385 | 19 | |
| α-helix | 394-417 | 24 | |
| α-helix | 418-422 | 5 | |
| α-helix | 427-445 | 19 | |
| α-helix | 452-455 | 4 | |
| α-helix | 457-476 | 20 | |
| α-helix | 480-494 | 15 | |
| α-helix | 502-523 | 22 | |
| β-strand | 527 | 1 | 8 |
| β-strand | 534 | 1 | 8 |
| α-helix | 536-552 | 17 | |
| α-helix | 555-560 | 6 | |
| α-helix | 589-600 | 12 | |
| α-helix | 603-606 | 4 | |
Chain C: 31 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-20 | 6 | |
| α-helix | 33-36 | 4 | |
| α-helix | 39-43 | 5 | |
| β-strand | 50-51 | 2 | 9 |
| α-helix | 57-69 | 13 | |
| α-helix | 72-76 | 5 | |
| α-helix | 97-105 | 9 | |
| α-helix | 108-121 | 14 | |
| α-helix | 123-127 | 5 | |
| α-helix | 133-148 | 16 | |
| β-strand | 153 | 1 | 7 |
| α-helix | 154-173 | 20 | |
| α-helix | 176-182 | 7 | |
| α-helix | 185-191 | 7 | |
| α-helix | 204-223 | 20 | |
| α-helix | 232-240 | 9 | |
| α-helix | 245-248 | 4 | |
| α-helix | 250-264 | 15 | |
| α-helix | 280-302 | 23 | |
| α-helix | 317-318 | 2 | |
| α-helix | 320-326 | 7 | |
| α-helix | 340-355 | 16 | |
| α-helix | 364-365 | 2 | |
| α-helix | 369-386 | 18 | |
| α-helix | 394-422 | 29 | |
| α-helix | 427-444 | 18 | |
| α-helix | 451-454 | 4 | |
| α-helix | 457-476 | 20 | |
| α-helix | 480-494 | 15 | |
| α-helix | 502-523 | 22 | |
| β-strand | 527-528 | 2 | 9 |
| α-helix | 536-552 | 17 | |
| α-helix | 555-562 | 8 | |
| α-helix | 589-600 | 12 | |
Chain D: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 10 |
| β-strand | 15-19 | 5 | 10 |
| α-helix | 22-25 | 4 | |
| α-helix | 27-32 | 6 | |
| β-strand | 75-78 | 4 | 10 |
| α-helix | 84-97 | 14 | |
| α-helix | 114-117 | 4 | |
| α-helix | 118-123 | 6 | |
| α-helix | 128-141 | 14 | |
| α-helix | 144-158 | 15 | |
| α-helix | 163-168 | 6 | |
| α-helix | 178-188 | 11 | |
Chain E: 26 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-34 | 4 | |
| α-helix | 39-58 | 20 | |
| β-strand | 80 | 1 | 11 |
| α-helix | 82-89 | 8 | |
| α-helix | 90-94 | 5 | |
| α-helix | 99-101 | 3 | |
| α-helix | 108-138 | 31 | |
| β-strand | 144 | 1 | 11 |
| α-helix | 148-167 | 20 | |
| α-helix | 184-191 | 8 | |
| α-helix | 208-223 | 16 | |
| α-helix | 228-232 | 5 | |
| β-strand | 235 | 1 | 12 |
| α-helix | 236-238 | 3 | |
| β-strand | 240 | 1 | 13 |
| β-strand | 250 | 1 | 13 |
| β-strand | 253-254 | 2 | 14 |
| β-strand | 267-268 | 2 | 14 |
| α-helix | 282-294 | 13 | |
| β-strand | 322 | 1 | 12 |
| α-helix | 335-348 | 14 | |
| α-helix | 356-359 | 4 | |
| α-helix | 372-377 | 6 | |
| α-helix | 381-383 | 3 | |
| α-helix | 401-405 | 5 | |
| α-helix | 419-421 | 3 | |
| α-helix | 426-428 | 3 | |
| α-helix | 429-432 | 4 | |
| α-helix | 437-442 | 6 | |
| α-helix | 452-478 | 27 | |
| α-helix | 483-485 | 3 | |
| α-helix | 493-502 | 10 | |
| β-strand | 511 | 1 | 15 |
| α-helix | 521-524 | 4 | |
| β-strand | 526 | 1 | 15 |
| α-helix | 527-533 | 7 | |
Chain H: 23 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-11 | 6 | |
| α-helix | 14-23 | 10 | |
| β-strand | 45-46 | 2 | 16 |
| α-helix | 58-65 | 8 | |
| α-helix | 67-69 | 3 | |
| α-helix | 74-77 | 4 | |
| α-helix | 81-93 | 13 | |
| α-helix | 94-96 | 3 | |
| α-helix | 98-110 | 13 | |
| β-strand | 118-120 | 3 | 17 |
| β-strand | 129-132 | 4 | 17 |
| β-strand | 138-140 | 3 | 17 |
| α-helix | 144-147 | 4 | |
| α-helix | 148-152 | 5 | |
| α-helix | 160-163 | 4 | |
| β-strand | 168 | 1 | 18 |
| β-strand | 169 | 1 | 17 |
| α-helix | 177-189 | 13 | |
| β-strand | 196 | 1 | 18 |
| α-helix | 258-267 | 10 | |
| α-helix | 268-270 | 3 | |
| β-strand | 276-278 | 3 | 19 |
| α-helix | 281-287 | 7 | |
| α-helix | 303-308 | 6 | |
| β-strand | 311-317 | 7 | 19 |
| β-strand | 326 | 1 | 20 |
| β-strand | 336-342 | 7 | 19 |
| β-strand | 344-345 | 2 | 21 |
| α-helix | 347-349 | 3 | |
| β-strand | 350 | 1 | 20 |
| β-strand | 358-361 | 4 | 19 |
| β-strand | 366-367 | 2 | 21 |
| α-helix | 372-379 | 8 | |
| α-helix | 384-385 | 2 | |
| α-helix | 386-390 | 5 | |
| β-strand | 410-411 | 2 | 22 |
| α-helix | 424-432 | 9 | |
| β-strand | 439 | 1 | 19 |
| β-strand | 442 | 1 | 19 |
| β-strand | 452-453 | 2 | 22 |
| α-helix | 456-459 | 4 | |
| α-helix | 460-462 | 3 | |
| β-strand | 475-476 | 2 | 22 |
Chain I: 35 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-20 | 6 | |
| α-helix | 31-35 | 5 | |
| α-helix | 39-43 | 5 | |
| α-helix | 57-70 | 14 | |
| α-helix | 71-76 | 6 | |
| α-helix | 77-78 | 2 | |
| β-strand | 89 | 1 | 23 |
| α-helix | 99-105 | 7 | |
| α-helix | 108-121 | 14 | |
| α-helix | 125-129 | 5 | |
| α-helix | 134-143 | 10 | |
| α-helix | 154-173 | 20 | |
| α-helix | 176-182 | 7 | |
| α-helix | 186-192 | 7 | |
| α-helix | 200-202 | 3 | |
| α-helix | 204-223 | 20 | |
| α-helix | 231-241 | 11 | |
| α-helix | 245-248 | 4 | |
| α-helix | 250-267 | 18 | |
| α-helix | 280-302 | 23 | |
| α-helix | 343-355 | 13 | |
| α-helix | 363-366 | 4 | |
| α-helix | 367-381 | 15 | |
| α-helix | 394-421 | 28 | |
| α-helix | 427-444 | 18 | |
| α-helix | 451-453 | 3 | |
| α-helix | 457-476 | 20 | |
| α-helix | 480-494 | 15 | |
| α-helix | 502-523 | 22 | |
| α-helix | 525-526 | 2 | |
| β-strand | 527 | 1 | 24 |
| α-helix | 528 | 1 | |
| β-strand | 534 | 1 | 24 |
| α-helix | 536-552 | 17 | |
| α-helix | 556-559 | 4 | |
| α-helix | 589-592 | 4 | |
| α-helix | 594-600 | 7 | |
| α-helix | 603-606 | 4 | |
Chain J: 31 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-19 | 5 | |
| β-strand | 51 | 1 | 25 |
| α-helix | 57-60 | 4 | |
| α-helix | 64-68 | 5 | |
| α-helix | 69-79 | 11 | |
| α-helix | 97-105 | 9 | |
| α-helix | 108-121 | 14 | |
| α-helix | 123-129 | 7 | |
| α-helix | 133-143 | 11 | |
| β-strand | 153 | 1 | 23 |
| α-helix | 154-172 | 19 | |
| α-helix | 176-182 | 7 | |
| α-helix | 189-192 | 4 | |
| α-helix | 205-223 | 19 | |
| α-helix | 231-240 | 10 | |
| α-helix | 245-248 | 4 | |
| α-helix | 250-266 | 17 | |
| α-helix | 280-302 | 23 | |
| α-helix | 343-353 | 11 | |
| α-helix | 364-366 | 3 | |
| α-helix | 367-382 | 16 | |
| 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 | 480-495 | 16 | |
| α-helix | 498-500 | 3 | |
| α-helix | 502-523 | 22 | |
| β-strand | 527 | 1 | 25 |
| β-strand | 534 | 1 | 25 |
| α-helix | 536-551 | 16 | |
| α-helix | 555-561 | 7 | |
| α-helix | 593-600 | 8 | |
| α-helix | 603-606 | 4 | |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Centromere DNA-binding protein complex CBF3 subunit C | A, H | protein | 478 | Saccharomyces cerevisiae | P35203 (AlphaFold model) |
| Centromere DNA-binding protein complex CBF3 subunit B | B, C, I, J | protein | 608 | Saccharomyces cerevisiae | P40969 (AlphaFold model) |
| Suppressor of kinetochore protein 1 | D, K | protein | 194 | Saccharomyces cerevisiae | P52286 (AlphaFold model) |
| Centromere DNA-binding protein complex CBF3 subunit A | E, L | protein | 956 | Saccharomyces cerevisiae | P32504 (AlphaFold model) |
| DNA (52-mer) | F | DNA | 52 | Saccharomyces cerevisiae | |
| DNA (52-mer) | G | DNA | 52 | Saccharomyces cerevisiae | |
Sequence of entity 1 (A, H), FASTA
>6GYS_1 Centromere DNA-binding protein complex CBF3 subunit C (chains A, H)
MPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSK
KLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEW
TYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQLV
DKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASKR
SHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKT
ISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLT
MKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEINQ
ITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVI
Sequence of entity 2 (B, C, I, J), FASTA
>6GYS_2 Centromere DNA-binding protein complex CBF3 subunit B (chains B, C, I, J)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPD
LLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAME
NLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLA
EIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLIL
ATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCD
YLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLN
KSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLI
YYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESA
AVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKI
LQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSE
YNISDILS
Sequence of entity 3 (D, K), FASTA
>6GYS_3 Suppressor of kinetochore protein 1 (chains D, K)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR
Sequence of entity 4 (E, L), FASTA
>6GYS_4 Centromere DNA-binding protein complex CBF3 subunit A (chains E, L)
MRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQ
IIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIA
TLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQV
LCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSLK
LGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSV
SKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFN
KCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTNA
KKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFFP
NHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQ
LTFASSHNPDTHPTQKQESEGPLQMSQLDTTQLNELLKQQSFEYVQFQTLSNFQILLSVF
NKIFEKLEMKKSSRGYILHQLNLFKITLDERIKKSKIDDADKFIRDNQPIKKEENIVNED
GPNTSRRTKRPKQIRLLSIADSSDESSTEDSNVFKKDGESIEDGAYGENEDENDSEMQEQ
LKSMINELINSKISTFLRDQMDQFELKINALLDKILEEKVTRIIEQKLGSHTGKFSTLKR
PQLYMTEEHNVGFDMEVPKKLRTSGKYAETVKDNDDHQAMSTTASPSPEQDQEAKSYTDE
QEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGNKSWRANCEALYKERKSIVEFY
IYLVNHESLDRYKAVDICEKLRDQNEGSFSRLAKFLRKWRHDHQNSFDGLLVYLSN
Sequence of entity 5 (F), FASTA
>6GYS_5 DNA (52-MER) (chains F)
TTAAAATATTAGTGTATTTGATTTCCGAAAGTTAAAAAAGAAATAGTAAGAA
Sequence of entity 6 (G), FASTA
>6GYS_6 DNA (52-MER) (chains G)
TTCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTAATATTTTAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
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 P35203 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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
Browse structure collections
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