10EH: De novo assembled CBF3-CEN complex

De novo assembled CBF3-CEN complex. Determined by electron microscopy at 3.5 Å resolution. Released 1 Jul 2026.

Method
Electron microscopy
Resolution
3.5 Å
Organisms
Saccharomyces cerevisiae, synthetic construct
Chains
15
Atoms
40,149
Mol. weight
1317.41 kDa
Ligands
ZN
Released
1 Jul 2026

Explore 10EH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

10EH contains 269 α-helices and 99 β-strands across 13 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: 26 helices, 7 β-strands

ElementResiduesLengthSheet
α-helix27-348
α-helix39-5820
α-helix82-887
α-helix89-946
α-helix116-13116
α-helix132-1365
α-helix148-17427
α-helix178-1814
α-helix184-19310
α-helix208-22316
α-helix228-2314
β-strand235120
β-strand239-240221
β-strand249-256821
β-strand264-272921
α-helix282-29514
β-strand322120
α-helix335-34814
α-helix356-3594
β-strand368-370321
α-helix371-3777
α-helix396-3983
α-helix401-4055
α-helix406-4083
α-helix421-4233
α-helix426-4283
α-helix429-4313
α-helix437-4448
α-helix452-47827
α-helix494-50310
α-helix520-5223
α-helix527-5315
β-strand53612
Chain A: 26 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix29-357
α-helix39-5820
β-strand72-7431
α-helix82-898
α-helix90-945
α-helix111-13929
α-helix148-17326
β-strand17612
α-helix184-19310
α-helix208-22417
α-helix228-2314
β-strand23513
β-strand239-24134
β-strand249-25244
β-strand255-25625
β-strand264-26855
β-strand269-27244
α-helix282-29514
β-strand29716
β-strand30116
β-strand32213
α-helix332-3343
α-helix335-34915
α-helix356-3594
β-strand368-37035
α-helix371-3788
α-helix396-3983
α-helix401-4077
α-helix426-4283
α-helix431-4344
α-helix437-44610
α-helix447-4493
α-helix452-47827
α-helix483-4853
α-helix488-4914
α-helix493-50210
β-strand51117
α-helix522-5254
β-strand52617
α-helix527-5315
Chain b: 33 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand14122
β-strand19122
α-helix58-6811
α-helix69-757
β-strand89123
α-helix901
α-helix93-10513
α-helix108-12114
α-helix123-1264
α-helix133-14614
β-strand153124
α-helix154-17219
α-helix176-1827
α-helix186-1927
α-helix200-2045
α-helix205-22218
α-helix231-24212
α-helix245-2484
α-helix250-26718
α-helix274-2752
α-helix280-30223
β-strand305125
β-strand308125
α-helix313-3153
β-strand316126
α-helix323-3275
β-strand332126
α-helix334-3363
α-helix341-35616
α-helix363-3664
α-helix367-38620
α-helix394-42128
α-helix427-44418
α-helix451-4555
α-helix457-47418
α-helix480-49516
α-helix502-52322
α-helix525-5262
β-strand527-528227
β-strand533-534227
α-helix536-55116
α-helix555-5606
α-helix591-60010
Chain B: 36 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand2-328
α-helix41
α-helix16-194
α-helix58-6912
α-helix70-745
α-helix881
β-strand8919
α-helix901
α-helix94-10512
α-helix108-12013
α-helix127-1304
α-helix133-14715
β-strand153110
α-helix154-17219
α-helix176-1827
α-helix186-1927
α-helix200-2045
α-helix205-22218
α-helix225-2273
α-helix231-24010
α-helix245-2484
α-helix250-26617
α-helix280-30223
α-helix313-3153
β-strand316111
β-strand332111
α-helix334-3363
α-helix341-35616
α-helix364-3663
α-helix367-38620
α-helix394-41724
α-helix418-4225
α-helix427-44317
α-helix448-4558
α-helix457-47620
α-helix480-49415
α-helix502-52322
β-strand527-52828
β-strand532-53438
α-helix536-55116
α-helix555-5617
α-helix590-60011
α-helix603-6064
Chain c: 36 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix15-195
α-helix31-355
α-helix39-457
α-helix58-6811
α-helix69-757
α-helix881
β-strand89124
α-helix901
α-helix94-10512
α-helix108-12114
α-helix123-1297
α-helix134-14512
β-strand153123
α-helix154-17219
α-helix176-1805
α-helix186-1927
α-helix200-2045
α-helix205-22218
α-helix225-2273
α-helix231-24212
α-helix245-2484
α-helix250-26617
α-helix280-30223
β-strand305128
β-strand308128
α-helix342-35615
α-helix367-38418
α-helix394-41724
α-helix418-4225
α-helix427-44317
α-helix448-4558
α-helix457-47620
α-helix482-49514
α-helix498-5003
α-helix502-52322
α-helix525-5262
β-strand527-528229
β-strand533-534229
α-helix536-55217
α-helix555-5628
α-helix589-60012
α-helix604-6063
Chain C: 34 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix15-206
α-helix31-355
α-helix41-433
β-strand50112
α-helix58-6912
α-helix70-767
β-strand89110
α-helix90-912
α-helix93-10513
α-helix108-12114
α-helix123-1264
α-helix134-14613
β-strand15319
α-helix154-17320
α-helix176-1827
α-helix186-1927
α-helix200-2023
α-helix204-22320
α-helix231-24010
α-helix250-26415
α-helix280-30122
α-helix317-3182
α-helix320-3289
α-helix342-35615
α-helix364-3663
α-helix367-38519
α-helix394-42128
α-helix428-44417
α-helix451-4555
α-helix458-47619
α-helix480-49213
α-helix502-52322
α-helix525-5262
β-strand527-528212
β-strand533-534212
α-helix536-55217
α-helix556-5627
α-helix590-60011
α-helix603-6053
Chain d: 24 helices, 21 β-strands
ElementResiduesLengthSheet
α-helix8-114
α-helix131
α-helix33-353
α-helix36-405
α-helix59-657
α-helix67-748
α-helix81-9414
α-helix98-10912
α-helix116-1183
β-strand119-123530
β-strand126-132730
β-strand138-143630
α-helix144-1474
α-helix148-1525
α-helix163-1653
β-strand168-171430
α-helix177-18812
α-helix192-1954
β-strand196-201630
α-helix258-2658
α-helix267-2693
β-strand275-279530
α-helix282-2832
α-helix284-2885
α-helix303-3075
β-strand311-315530
β-strand319131
β-strand327132
β-strand336-340530
β-strand344-346331
β-strand351132
β-strand358-362530
β-strand366-368331
α-helix372-3809
α-helix384-3918
β-strand392-394333
α-helix400-4034
β-strand409-413533
α-helix420-43415
β-strand439-443530
β-strand447-449331
β-strand453-454233
α-helix456-4605
β-strand464-467430
β-strand474-477433
Chain D: 25 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix6-116
α-helix14-2411
α-helix32-354
α-helix36-405
β-strand44-4631
α-helix58-658
α-helix68-703
α-helix71-744
α-helix75-773
α-helix81-9010
α-helix98-10912
α-helix116-1183
β-strand119-123513
β-strand126-130513
β-strand132114
β-strand138114
β-strand143113
α-helix144-1474
α-helix148-1525
α-helix159-1624
β-strand168-170315
α-helix177-19014
β-strand196-201615
α-helix258-2669
α-helix267-2693
β-strand276-279415
α-helix281-2877
α-helix303-3086
β-strand311-319915
β-strand326-327216
β-strand336-344915
β-strand345-346217
α-helix347-3493
β-strand350-351216
β-strand358-364715
β-strand366-368317
α-helix372-3809
α-helix384-3907
β-strand392-394318
α-helix398-4025
β-strand409-413518
α-helix420-43415
β-strand439-443515
β-strand447-449317
β-strand453-454218
α-helix456-4594
β-strand464-467415
β-strand474-477418

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Centromere DNA-binding protein complex CBF3 subunit AA, H, I, J, aprotein956Saccharomyces cerevisiaeP32504 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit BB, C, b, cprotein608Saccharomyces cerevisiaeP40969 (AlphaFold model)
Centromere DNA-binding protein complex CBF3 subunit CD, dprotein478Saccharomyces cerevisiaeP35203 (AlphaFold model)
Suppressor of kinetochore protein 1E, eprotein194Saccharomyces cerevisiaeP52286 (AlphaFold model)
DNA (44-mer)FDNA508synthetic construct
DNA (44-mer)GDNA508synthetic construct
Sequence of entity 1 (A, H, I, J, a), FASTA
>10EH_1 Centromere DNA-binding protein complex CBF3 subunit A (chains A, H, I, J, a)
MRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQ
IIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIA
TLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQV
LCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSLK
LGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSV
SKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFN
KCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTNA
KKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFFP
NHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQ
LTFASSHNPDTHPTQKQESEGPLQMSQLDTTQLNELLKQQSFEYVQFQTLSNFQILLSVF
NKIFEKLEMKKSSRGYILHQLNLFKITLDERIKKSKIDDADKFIRDNQPIKKEENIVNED
GPNTSRRTKRPKQIRLLSIADSSDESSTEDSNVFKKDGESIEDGAYGENEDENDSEMQEQ
LKSMINELINSKISTFLRDQMDQFELKINALLDKILEEKVTRIIEQKLGSHTGKFSTLKR
PQLYMTEEHNVGFDMEVPKKLRTSGKYAETVKDNDDHQAMSTTASPSPEQDQEAKSYTDE
QEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGNKSWRANCEALYKERKSIVEFY
IYLVNHESLDRYKAVDICEKLRDQNEGSFSRLAKFLRKWRHDHQNSFDGLLVYLSN
Sequence of entity 2 (B, C, b, c), FASTA
>10EH_2 Centromere DNA-binding protein complex CBF3 subunit B (chains B, C, b, c)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPD
LLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAME
NLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLA
EIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLIL
ATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCD
YLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLN
KSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLI
YYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESA
AVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKI
LQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSE
YNISDILS
Sequence of entity 3 (D, d), FASTA
>10EH_3 Centromere DNA-binding protein complex CBF3 subunit C (chains D, d)
MPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSK
KLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEW
TYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQLV
DKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASKR
SHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKT
ISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLT
MKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEINQ
ITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVI
Sequence of entity 4 (E, e), FASTA
>10EH_4 Suppressor of kinetochore protein 1 (chains E, e)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR
Sequence of entity 5 (F), FASTA
>10EH_5 DNA (44-MER) (chains F)
ATCAGCGCCAAACAATATGGAAAATCCACAGAAAGCTATTCATTGAAAAAATAGTACAAA
TAAGTCACATGATGATATTTGATTTTATTATATTTTTAAAAAAAGTAAAAAATAAAAAGT
AGTTTATTTTTAAAAAATAAAATTTAAAATATTAGTGTATTTGATTTCCGAAAGTTAAAA
AAGAAATAGTAAGAAATATATATTTCATTGAATGGATATATGAAACGTTTACTGGTGGAA
GGCCGGCGGTTGTTTGCAAGACCGAGAAAAGGCTAGCAAGAATCGGGTCATTGTAGCGTA
TGCGCCTGTGAACATTCTCTTCAACAAGTTTGATTCCATTGCGGTGAAATGGTAAAAGTC
AACCCCCTGCGATGTATATTTTCCTGTACAATCAATCAAAAAGCCAAATGATTTAGCATT
ATCTTTACATCTTGTTATTTTACAGATTTTATGTTTAGATCTTTTATGCTTGCTTTTCAA
AAGGCCTGCAGGCAAGTGCACAAACAAT
Sequence of entity 6 (G), FASTA
>10EH_6 DNA (44-MER) (chains G)
ATTGTTTGTGCACTTGCCTGCAGGCCTTTTGAAAAGCAAGCATAAAAGATCTAAACATAA
AATCTGTAAAATAACAAGATGTAAAGATAATGCTAAATCATTTGGCTTTTTGATTGATTG
TACAGGAAAATATACATCGCAGGGGGTTGACTTTTACCATTTCACCGCAATGGAATCAAA
CTTGTTGAAGAGAATGTTCACAGGCGCATACGCTACAATGACCCGATTCTTGCTAGCCTT
TTCTCGGTCTTGCAAACAACCGCCGGCCTTCCACCAGTAAACGTTTCATATATCCATTCA
ATGAAATATATATTTCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTAATAT
TTTAAATTTTATTTTTTAAAAATAAACTACTTTTTATTTTTTACTTTTTTTAAAAATATA
ATAAAATCAAATATCATCATGTGACTTATTTGTACTATTTTTTCAATGAATAGCTTTCTG
TGGATTTTCCATATTGTTTGGCGCTGAT

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1

Primary citation

Native yeast kinetochore structures identify an essential inner kinetochore interaction. Mengqiu, J., Sue, B. To be published.

Other PDB entries of the same protein (UniProt P32504 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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