2024-10-23 REL PDBe PDBe PDBe 2018-06-13 2018-07-04 2018-08-01 2024-10-23 Biotechnology and Biological Sciences Research Council BB/J007595/1 United Kingdom Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Zhang WJ Lukoynova N Centromere, CDEIII-binding, LRR domain, DNA BINDING PROTEIN Zhang W Lukoynova N Miah S Lucas J Vaughan CK Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. Cell Rep US 24 744 754 2018 30021170 doi:10.1016/j.celrep.2018.06.068 2211-1247 EMD-4241 other EM volume
The map of the CBF3 core complex
 6gsa FULLOVERLAP Core CBF3 in complex with Ndc10 D1-2 Core CBF3 in complex with Ndc10 D1-2 0 1 2 3 4
The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length heterodimer of Skp1 and Ctf13, and a monomeric construct Ndc10 comprising domains 1-2.
Saccharomyces cerevisiae 0.286 Centromere DNA-binding protein complex CBF3 subunit B Saccharomyces cerevisiae 0.06845412499999999
N-terminal polyhistidine purification tagTruncation of the binuclear zinc cluster domain
2 Saccharomyces cerevisiae LEVO MGGSSHHHHHHSSGLVPRGSHMKLITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMN YLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLAEIFS VYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTF KNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVL YWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLIYYDT ADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKL DKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENN TEPSDFRTIVEEFQSEYNISDILS P40969 Suppressor of kinetochore protein 1 Saccharomyces cerevisiae 0.022558451 1 Saccharomyces cerevisiae LEVO MGVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSKDNNNGDDDDEDDDEIVMPV PNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIR GRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDRGS P52286 Centromere DNA-binding protein complex CBF3 subunit C Saccharomyces cerevisiae 0.060899961
C-terminal CBP purification tag
1 Saccharomyces cerevisiae LEVO MGPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSKKLLRYMYPVFATYLNIFEY SPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEWTYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDE LDLLNVSNIQFNIDNLTPQLVDKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASK RSHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKTISYIVKRRINEIRLSRMNQ ISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLTMKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKF TKFFNLRHTRIKELDKSEINQITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVIG SRSGSENLYFQGSKRRWKKNFIAVSAANRFKKISSSGAL P35203 Centromere DNA-binding protein complex CBF3 subunit A Saccharomyces cerevisiae 0.066159578
Domains 1-2 of Ndc10 with a non-cleavable C-terminal StrepII tag
1 Saccharomyces cerevisiae LEVO MGRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQIIPTPEDNSVNSVPYKDLP ISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIATLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHT HWIDSQKAITTNETNNTNTQVLCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSL KLGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSVSKGDGFPNLNADENGSLLQ DIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFNKCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKI PFDFKKIMNFKSPYTSYSTNAKKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFF PNHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQLTFASSHNPDTHPWSHPQF EK P32504 singleParticle particle 0.15 8.0 200.0 NaCl sodium chloride 15.0 Tris base 2.0 DTT Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK I
The sample is homogeneous and well-dispersed on grids.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 47170.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-40 1 2003 50.0 1
The selected images were high-pass filtered and normalized.
214608
Number of particles after selection by 2D classification
Cryosparc was used to generate a startup model from a smaller dataset collected in-house. This was then low pass filtered to 60 Angstroms
 1 C1 FOURIER SPACE 4.2 FSC 0.143 CUT-OFF RELION 2.0 56509 ANGULAR RECONSTITUTION RELION 2.0 ANGULAR RECONSTITUTION RELION 2.0 6 RELION 2.0 emd_0051.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 271.36 271.36 271.36 90.0 90.0 90.0 X Y Z -0.02745911 0.09228461 0.00013709656 0.0042895144 1.06 1.06 1.06 0.0174 AUTHOR Reconstruction of the CBF3CCdeltaN (Core complex of CBF3 comprising the homodimer of Cep3deltaN and the heterodimer of Skp1-Ctf13) in complex with domains 1-2 of Ndc10
"Fit in map" function used to place 6FE8 and 4ACO with out further refinement or model building