Cooperation between the intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly

2024-11-13 REL PDBe PDBe PDBe 2021-04-01 2022-04-13 2022-04-13 2024-11-13 Ministry of Education, Youth and Sports of the Czech Republic LM20115043 Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LM20115070 Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LM20115042 Czech Republic European Research Council (ERC) 649030 Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LQ1601 Czech Republic Czech Science Foundation GA18-11397S Czech Republic Cooperation between the intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly Kasiliauskaite A Kubicek K Spt6, elongation factor, RNA Pol II, nucleosome, CTD, CHAPERONE Kasiliauskaite A Kubicek K Klumpler T Zanova M Zapletal D Koutna E Novacek J Stefl R Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res. UK 50 5961 5973 2022 35640611 doi:10.1093/nar/gkac451 1362-4962 0389 NARHAD 7o3d FULLOVERLAP Structure of elongation factor Spt6 Structure of elongation factor Spt6 0 1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Transcription elongation factor SPT6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.13492303099999997

the sequence stretches of the sample that do not make part of the coordinates are flexible regions that were not observed in the cryoEM map

1 Escherichia coli B LEVO GIDPFTDIYDLEDLKKNLMTEGDMKIRKTDIPERYQELRAGITDYGNMSSEDQELERNWIAEKISVDKNFDANYDLTEFK EAIGNAIKFITKENLEVPFIYAYRRNYISSREKDGFLLTEDDLWDIVSLDIEFHSLVNKKDYVQRFYAELHIDDPIVTEY FKNQNTASIAELNSLQDIYDYLEFKYANEINEMFINHTGKTGKKHLKNSSYEKFKASPLYQAVSDIGISAEDVGENISSQ HQIHPPVDHPSSKPVEVIESILNANSGDLQVFTSNTKLAIDTVQKYYSLELSKNTKIREKVRSDFSKYYLADVVLTAKGK KEIQKGSLYEDIKYAINRTPMHFRRDPDVFLKMVEAESLNLLSVKLHMSSQAQYIEHLFQIALETTNTSDIAIEWNNFRK LAFNQAMDKIFQDISQEVKDNLTKNCQKLVAKTVRHKFMTKLDQAPFIPNVRDPKIPKILSLTCGQGRFGADAIIAVYVN RKGDFIRDYKIVDNPFDKTNPEKFEDTLDNIIQSCQPNAIGINGPNPKTQKFYKRLQEVLHKKQIVDSRGHTIPIIYVED EVAIRYQNSERAAQEFPNKPPLVKYCIALARYMHSPLLEYANLTSEEVRSLSIHPHQNLLSSEQLSWALETAFVDIVNLV SVEVNKATDNNYYASALKYISGFGKRKAIDFLQSLQRLNEPLLARQQLITHNILHKTIFMNSAGFLYISWNEKRQKYEDL EHDQLDSTRIHPEDYHLATKVAADALEYDPDTIAEKEEQGTMSEFIELLREDPDRRAKLESLNLESYAEELEKNTGLRKL NNLNTIVLELLDGFEELRNDFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQ LRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHDVKQQYVPISYSKDPSIWDLKQELEDAEEERKLMMAEARAKRTH RVINHPYYFPFNGRQAEDYLRSKERGEFVIRQSSRGDDHLVITWKLDKDLFQHIDIQELEKENPLALGKVLIVDNQKYND LDQIIVEYLQNKVRLLNEMTSSEKFKSGTKKDVVKFIEDYSRVNPNKSVYYFSLNHDNPGWFYLMFKINANSKLYTWNVK LTNTGYFLVNYNYPSVIQLCNGFKTLLKSNSSKNRMNNYR P23615 singleParticle particle 0.15 7.5 20.0 HEPES HEPES Quantifoil R2/1 COPPER 300 GLOW DISCHARGE 30 OTHER 0.007 ETHANE 100 277 FEI VITROBOT MARK IV

homogeneous monodisperse sample

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 30.0 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3840 3710 1-40 1 13807 5.0 55.0 1 2995892 3PSI

Initial PDB coordinates of the Spt6 structure comprising residues 298-1248 were produced from PDBs of a crystal structure of Spt6, namely 3PSI and 3PSF. The PDB and the cryoSPARC sharpened electron density map were imported into the program Coot and the tool 'Real Space Refine Zone' was used to achiev e optimal fit of the PDB coordinates within the map. Low-resolution regions of the map (regions corresponding to residues: 1226-1243 and the S1-domain) were also excluded from the PDB and were docked with a rigid body strategy using Phenix once the fit of the well-resolved regions exhibited no clashes and deviations.

313 C1 3.71 FSC 0.143 CUT-OFF cryoSPARC 3.1 718639 MAXIMUM LIKELIHOOD cryoSPARC 3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.1 313 2296.0 cryoSPARC 3.1 emd_12704.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.968 211.968 211.968 90.0 90.0 90.0 X Y Z -0.46966928 0.6867795 -0.0013449175 0.01961691 0.828 0.828 0.828 0.164 AUTHOR ::::EMDATABANK.org::::EMD-12704:::: Cryosparc sharpened electron density map 3PSI A 1127-1219 PDB experimental model 3PSF A 298-1248 PDB experimental model FLEXIBLE FIT Correlation coefficients REAL emd_12704_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.968 211.968 211.968 90.0 90.0 90.0 X Y Z -0.2751841 0.37144205 -0.00083686993 0.03412982 0.828 0.828 0.828 AUTHOR ::::EMDATABANK.org::::EMD-12704:::: emd_12704_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.968 211.968 211.968 90.0 90.0 90.0 X Y Z -0.23643766 0.35551584 -0.00083645614 0.03407256 0.828 0.828 0.828 AUTHOR ::::EMDATABANK.org::::EMD-12704::::