2026-04-22 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2025-07-28 2026-04-08 2026-04-08 2026-04-22 Cancer Research UK C576/A25675 United Kingdom Cancer Research UK C576/A14109 United Kingdom UK Research and Innovation (UKRI) MC_UP_1201/6 United Kingdom Turner NN Barford D Kinetochore, chromosome segregation, mitosis, cell cycle Turner NN Zhang Z Yang J Muir KW McLaughlin SH Morgan T Barford D J.Cell Biol. US 225 2026 41956986 doi:10.1083/jcb.202506015 1540-8140 2019 JCLBA3 EMD-54576 consensus EM volume

EMD-54576 is the consensus map of the Saccharomyces cerevisiae KMN junction complex used to generate this composite cryo-EM density map.

EMD-54577 focused EM volume

EMD-54577 is a component map of the base of this deposition derived from multibody refinement. It is a cryo-EM density map of the base of the Saccharomyces cerevisiae KMN complex.

EMD-54578 focused EM volume

EMD-54578 is a component map of the base of this deposition derived from multibody refinement. It is a cryo-EM density map of the apex of the Saccharomyces cerevisiae KMN complex.

9s4q FULLOVERLAP EMDB EMD-54576 consensus EM volume

EMD-54576 is the consensus map of the Saccharomyces cerevisiae KMN junction complex used to generate this composite cryo-EM density map.

EMDB EMD-54577 focused EM volume

EMD-54577 is a component map of the base of this deposition derived from multibody refinement. It is a cryo-EM density map of the base of the Saccharomyces cerevisiae KMN complex.

EMDB EMD-54578 focused EM volume

EMD-54578 is a component map of the base of this deposition derived from multibody refinement. It is a cryo-EM density map of the apex of the Saccharomyces cerevisiae KMN complex.

EMDB EMD-54579 associated EM volume

Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain

Saccharomyces cerevisiae outer kinetochore KMN junction complex Saccharomyces cerevisiae outer kinetochore KMN junction complex 0 1 2 3 4 5 6 7 8

Imaged sample also contained Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460), and Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) with a C-terminal HRV-3C protease cleavage site and twin-strep-tag II affinity tag.

Saccharomyces cerevisiae 288c 187.080 Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex 1 1 2 5 8 Saccharomyces cerevisiae 288c Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex 1 3 4

N-terminal truncation of Knl1(Spc105) residues 1-444

Saccharomyces cerevisiae 288c Saccharomyces cerevisiae outer kinetochore Ndc80c 1 6 7

Also contains Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460), and Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) with a C-terminal HRV-3C protease cleavage site and twin-strep-tag II affinity tag that were present in the imaged sample.

Saccharomyces cerevisiae 288c Kinetochore-associated protein NNF1 Saccharomyces cerevisiae S288C 0.023668541 1 Trichoplusia ni LEVO MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEFWTELCQREFKEIMEERNVEQ KLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVECHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVE VEKNEIGKMYDEYLGSHTDQPANVLLVQSLNDMVLELKENY P47149 Kinetochore-associated protein MTW1 Saccharomyces cerevisiae S288C 0.03329118 1 Trichoplusia ni LEVO MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEEIKSGVAKLESLLENSVDKNF DKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENELKKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRG FKQKLNELLKCKDDVQLQKILESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIR TNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL P39731 Outer kinetochore KNL1 complex subunit KRE28 Saccharomyces cerevisiae S288C 0.048468273

Fused to a C-terminal TEV protease cleavage site and twin-strep-tag II affinity tag.

1 Trichoplusia ni LEVO MDTGSASIKDYETVLTDIEDSIAVSSEEVLNNQELRLKNTLHEITSSILAINEENKFVNPLRNDESLDVEGKEVFVNPKI LSAKIKEFNKLMELLKLTYLEQETLDYFFRFTLSSTKPLQLDSEKDPQFVKLNERVNDLKEEISNVQESKIEQIKAEIQE TGHNFAERQDLINELYLEATGDIENCWDSLNELKNLTNKEDKNMMGEKDTILNSSDSDDFVEETYTNWQKLLFLQKQNQR LTKELKEMHEVKNQIIRKGEQSKKEDSGHLMANESELCQSINLLTKFWEKHFLLKGSKTTILNFEIFTQLGKVQFEIKDM QYIIAISLSDLKRPMIKDITILQKAGGNIVTDIEASSKFNNKYRNNTKVQIFEVMDDIISELTNEENLYFQSWSHPQFEK GGGSGGGSGGGSWSHPQFEK Q04431 Outer kinetochore KNL1 complex subunit SPC105 Saccharomyces cerevisiae S288C 0.055581046999999995

N-terminal truncation of residues 1-444

1 Trichoplusia ni LEVO MSGIALPTQDYTLREFINEVGVGFLDTKLIDDLDKKVNFPLNSFNFVENQRIDNVFSAFYIDIPILEVEAFRCKELWRSI NESKDKFKDFEAQIDKSHPPLLLQEYFSSDEKMKQLMRDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENLNTLKR EYEKLNEEVEKVNSIRGKIRKLNEAIKEEIRSLKNLPSDSYKPTLMNRIKIEAFKQELMEHSISLSSSNDFTQEMRSLKL AIAKKSNDILTLRSEVASIDKKIEKRKLFTRFDLPKLRDTLKILESLTGVRFLKFSKATLSIAFLQLDDLRVDINLANFK NNPLSSMKVMNDSNNDDMSYHLFTMLLKNVEAEHQDSMLSNLFFAMKKWRPLLKYIKLLKLLFPVKITQTEEEEALLQFK DYDRRNKTAFFYVISLVSFAQGVFSENGQIPMKVHISTQQDYSPSREVLSDRITHKISGVLPSFTKSRIHLEFT P53148 Kinetochore-associated protein DSN1 Saccharomyces cerevisiae S288C 0.065777023 1 Trichoplusia ni LEVO MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFENKQSVSNLSPDLKFKRHKNK HIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSGDATANATANATANATANVNASAMPAPYMPYYYYYHPMNAP TPAMIPYPGSPMHSIMPNSSLQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKS IGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRSLHKLELKAKNQEEEGELEHL TKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAIDWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDD DDDEVDYSEIQRSRRKFSERRKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSF SSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIETMRKISSETDDDHSQVINPQ QLLKGLSLSFSKKLDL P40568 Kinetochore protein SPC24 Saccharomyces cerevisiae S288C 0.024639813999999996 1 Trichoplusia ni LEVO MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESNKKLNAERINVAKLEGDLEYT NEESNEFGSKDELVKLLKDLDGLERNIVSLRSELDEKMKLYLKDSEIISTPNGSKIKAKVIEPELEEQSAVTPEANENIL KLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK Q04477 Kinetochore protein SPC25 Saccharomyces cerevisiae S288C 0.025280326 1 Trichoplusia ni LEVO MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQLHNQHQHLIDELQRLATQRTALQQQIHAAQQATNT TREQWRSYHERESELSRRQSTLAAQSRELDSLLQQRGKECVQLRARWAAQSGNDAAEVALYERLLQLRVLPGASDVHDVR FVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL P40014 Kinetochore-associated protein NSL1 Saccharomyces cerevisiae S288C 0.025448398 1 Trichoplusia ni LEVO MSQGQSKKLDVTVEQLRSIYHQFHDILEEKTDLHLPKKEYDDDAVRREVQIQLQEFLLSAMTMASKSLEVVNADTVGKTV KQLIMESQEKYMEPFDLDLNEQVRKMYQEWEDETVKVAQLRQTGPAKINEVYNNSKDEYLAQLDGRIGVLQARMMQQQSA DHDDSTDDADDHINWEHIKQDYVASLNELYQTQQDLPKVRYNVEKVKRLMDFLEED Q12143 singleParticle particle 7.5 20.0 HEPES 150.0 NaCl Sodium chloride 1.0 TCEP UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE

Edwards S150B glow discharger

ETHANE FEI VITROBOT MARK III TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.4000000000000001 3.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 40.0 1 2592458

Selected using Topaz particle picker trained on manually picked micrographs

CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 BACK PROJECTION 4.9 FSC 0.143 CUT-OFF RELION 5

Composite cryo-EM of two multibody refinement-derived map refined to the consensus map.

113688 MAXIMUM LIKELIHOOD RELION 5 MAXIMUM LIKELIHOOD RELION 5 4 28422.0 RELION 5

Focussed classification using Blush regularization.

AlphaFold in silico model FLEXIBLE FIT

Flexible fitting using Isolde, real-space refinement using Phenix

REAL