Multibody refinement cryo-EM density map of the base of the Saccharomyces cerevisiae KMN junction complex with Mis12c(Mtw1c) head 2 domain resolved

2026-04-22 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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 _citation_author.identifier_ORCID _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 _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-07-29 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 Multibody refinement cryo-EM density map of the base of the Saccharomyces cerevisiae KMN junction complex with Mis12c(Mtw1c) head 2 domain resolved Turner NN Barford D Kinetochore, chromosome segregation, mitosis, cell cycle Turner NN Zhang Z Yang J Muir KW McLaughlin SH Morgan T Barford D Assembly and phosphoregulatory mechanisms of the budding yeast outer kinetochore KMN complex. J.Cell Biol. US 225 2026 41956986 doi:10.1083/jcb.202506015 1540-8140 2019 JCLBA3 9s53 FULLOVERLAP EMDB EMD-54586 associated EM volume

Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing 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

Imaged sample also contained Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460); 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 kinetochore protein SPC24 (UniProtKB accession code Q04477); Saccharomyces cerevisiae Kinetochore protein SPC25 (UniProtKB accession code P40014); Saccharomyces cerevisiae outer kinetochore KNL1 complex subunit SPC105 (UniProtKB accession code P53148); and Saccharomyces cerevisiae outer kinetochore KNL1 complex subunit KRE28 (UniProtKB accession code Q04431) with a C-terminal TEV 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 3 4 Saccharomyces cerevisiae 288c Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex 1

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

Saccharomyces cerevisiae 288c Saccharomyces cerevisiae outer kinetochore Ndc80c 1 1 2 3 4 Saccharomyces cerevisiae 288c Kinetochore-associated protein DSN1 Saccharomyces cerevisiae S288C 0.065777023 1 Trichoplusia ni LEVO MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFENKQSVSNLSPDLKFKRHKNK HIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSGDATANATANATANATANVNASAMPAPYMPYYYYYHPMNAP TPAMIPYPGSPMHSIMPNSSLQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKS IGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRSLHKLELKAKNQEEEGELEHL TKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAIDWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDD DDDEVDYSEIQRSRRKFSERRKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSF SSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIETMRKISSETDDDHSQVINPQ QLLKGLSLSFSKKLDL P40568 Kinetochore-associated protein MTW1 Saccharomyces cerevisiae S288C S288c 0.03329118 1 Trichoplusia ni LEVO MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEEIKSGVAKLESLLENSVDKNF DKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENELKKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRG FKQKLNELLKCKDDVQLQKILESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIR TNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL P39731 Kinetochore-associated protein NNF1 Saccharomyces cerevisiae S288C S288c 0.023668541 1 Trichoplusia ni LEVO MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEFWTELCQREFKEIMEERNVEQ KLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVECHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVE VEKNEIGKMYDEYLGSHTDQPANVLLVQSLNDMVLELKENY P47149 Kinetochore-associated protein NSL1 Saccharomyces cerevisiae S288C 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 60 ETHANE 100 277.15 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) 1 26390 1.75 40.0 1 2592458

Selected using Topaz particle picker trained on manually picked micrographs

CTFFIND 4.1

CTFFIND 4.1 used as implemented in Relion 4.0

PHASE FLIPPING AND AMPLITUDE CORRECTION 1 6.5 FSC 0.143 CUT-OFF RELION 5.0

Multibody refinement in RELION 5.0 using Blush regularization

18160 MAXIMUM LIKELIHOOD RELION 5.0 MAXIMUM LIKELIHOOD 4 80269.0 RELION 5.0

Focussed classification using Blush regularization.

emd_54586.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 316.8 316.8 316.8 90.0 90.0 90.0 X Y Z -0.035442203 0.14359112 0.00016740304 0.0026028291 1.65 1.65 1.65 0.035 AUTHOR ::::EMDATABANK.org::::EMD-54586:::: Note not resampled to the consensus map to preserve higher resolution information. Dsn1 229-365 AlphaFold in silico model Nsl1 2-96 AlphaFold in silico model 9S4Q Mtw1 1-151 PDB experimental model 9S4Q Nnf1 1-153 PDB experimental model 9S4Q Dsn1 435-483 PDB experimental model 9S4Q Nsl1 97-159 PDB experimental model RIGID BODY FIT REAL emd_54586_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 316.8 316.8 316.8 90.0 90.0 90.0 X Y Z -0.14848514 0.16736227 0.00021920542 0.003449314 1.65 1.65 1.65 AUTHOR ::::EMDATABANK.org::::EMD-54586:::: Masked, post-processed and filtered map used for molecular model building. Note resampled to the consensus map for molecular model building. emd_54586_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 316.8 316.8 316.8 90.0 90.0 90.0 X Y Z 0.0 50.0 22.805250000000001 21.512667 1.65 1.65 1.65 AUTHOR ::::EMDATABANK.org::::EMD-54586:::: Local resolution file for the deposited map. emd_54586_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 316.8 316.8 316.8 90.0 90.0 90.0 X Y Z -0.048556533 0.13260701 0.00016801662 0.0041751815 1.65 1.65 1.65 AUTHOR ::::EMDATABANK.org::::EMD-54586:::: Note not resampled to the consensus map to preserve higher resolution information. emd_54586_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 316.8 316.8 316.8 90.0 90.0 90.0 X Y Z -0.047149125 0.13827817 0.00017774601 0.004151506 1.65 1.65 1.65 AUTHOR ::::EMDATABANK.org::::EMD-54586:::: Note not resampled to the consensus map to preserve higher resolution information.