2025-01-08 REL PDBe PDBe PDBe 2024-05-15 2024-11-13 2024-11-13 2025-01-08 Netherlands Organisation for Scientific Research (NWO) TOP 714.017.003 Netherlands Oncode Institute Netherlands Structure of Pol II-TC-NER-STK19 complex, focused on CSA-DDB1-DDA1-CSB Lee S-H Sixma TK Transcription-coupled DNA repair, TRANSCRIPTION Ramadhin AR Lee SH Zhou D Salmazo A Gonzalo-Hansen C van Sluis M Blom CMA Janssens RC Raams A Dekkers D Bezstarosti K Slade D Vermeulen W Pines A Demmers JAA Bernecky C Sixma TK Marteijn JA STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Mol.Cell US 84 4740 4757.e12 2024 39547223 doi:10.1016/j.molcel.2024.10.030 1097-2765 2168 MOCEFL Ternary complex of Pol II-TC-NER-STK19, focused on CSA-DDB1-DDA1-CSB Ternary complex of Pol II-TC-NER-STK19, focused on CSA-DDB1-DDA1-CSB 0 1 2 3 4 5 6 Homo sapiens 0.36 DNA excision repair protein ERCC-8 Homo sapiens
The construct contains a Strep tag II at the C-terminus
Spodoptera frugiperda LEVO MLGFLSARQTGLEDPLRLRRAESTRRVLGLELNKDRDVERIHGGGINTLDIEPVEGRYMLSGGSDGVIVLYDLENSSRQSYYTCKAVCSIGRDHPDVHRYSVETVQWYPHDTGMFTSSSFDKTLKVWDTNTLQTADVFNFEETVYSHHMSPVSTKHCLVAVGTRGPKVQLCDLKSGSCSHILQGHRQEILAVSWSPRYDYILATASADSRVKLWDVRRASGCLITLDQHNGKKSQAVESANTAHNGKVNGLCFTSDGLHLLTVGTDNRMRLWNSSNGENTLVNYGKVCNNSKKGLKFTVSCGCSSEFVFVPYGSTIAVYTVYSGEQITMLKGHYKTVDCCVFQSNFQELYSGSRDCNILAWVPSLYEPVPDDDETTTKSQLNPAFEDAWSSSDEEGGTSAWSHPQFEK Q13216 DNA damage-binding protein 1 Homo sapiens
The construct contains a His tag at the N-terminus
Spodoptera frugiperda LEVO MAHHHHHHSAALEVLFQGPGMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 DET1- and DDB1-associated protein 1 Homo sapiens
The construct contains a twin Strep tag and a flag tag at the C-terminus
Spodoptera frugiperda LEVO MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDTDVLFQGPGAWSHPQFEKGGGSGGGSGGGSWSHPQFEKGASGEDYKDDDDK Q9BW61 DNA excision repair protein ERCC-6 Homo sapiens
The construct contains a N-terminal HA tag and a C-terminal His tag
Spodoptera frugiperda LEVO MPNEGIPHSSQTQEQDCLQSQPVSNNEEMAIKQESGGDGEVEEYLSFRSVGDGLSTSAVGCASAAPRRGPALLHIDRHQIQAVEPSAQALELQGLGVDVYDQDVLEQGVLQQVDNAIHEASRASQLVDVEKEYRSVLDDLTSCTTSLRQINKIIEQLSPQAATSRDINRKLDSVKRQKYNKEQQLKKITAKQKHLQAILGGAEVKIELDHASLEEDAEPGPSSLGSMLMPVQETAWEELIRTGQMTPFGTQIPQKQEKKPRKIMLNEASGFEKYLADQAKLSFERKKQGCNKRAARKAPAPVTPPAPVQNKNKPNKKARVLSKKEERLKKHIKKLQKRALQFQGKVGLPKARRPWESDMRPEAEGDSEGEESEYFPTEEEEEEEDDEVEGAEADLSGDGTDYELKPLPKGGKRQKKVPVQEIDDDFFPSSGEEAEAASVGEGGGGGRKVGRYRDDGDEDYYKQRLRRWNKLRLQDKEKRLKLEDDSEESDAEFDEGFKVPGFLFKKLFKYQQTGVRWLWELHCQQAGGILGDEMGLGKTIQIIAFLAGLSYSKIRTRGSNYRFEGLGPTVIVCPTTVMHQWVKEFHTWWPPFRVAILHETGSYTHKKEKLIRDVAHCHGILITSYSYIRLMQDDISRYDWHYVILDEGHKIRNPNAAVTLACKQFRTPHRIILSGSPMQNNLRELWSLFDFIFPGKLGTLPVFMEQFSVPITMGGYSNASPVQVKTAYKCACVLRDTINPYLLRRMKSDVKMSLSLPDKNEQVLFCRLTDEQHKVYQNFVDSKEVYRILNGEMQIFSGLIALRKICNHPDLFSGGPKNLKGLPDDELEEDQFGYWKRSGKMIVVESLLKIWHKQGQRVLLFSQSRQMLDILEVFLRAQKYTYLKMDGTTTIASRQPLITRYNEDTSIFVFLLTTRVGGLGVNLTGANRVVIYDPDWNPSTDTQARERAWRIGQKKQVTVYRLLTAGTIEEKIYHRQIFKQFLTNRVLKDPKQRRFFKSNDLYELFTLTSPDASQSTETSAIFAGTGSDVQTPKCHLKRRIQPAFGADHDVPKRKKFPASNISVNDATSSEEKSEAKGAEVNAVTSNRSDPLKDDPHMSSNVTSNDRLGEETNAVSGPEELSVISGNGECSNSSGTGKTSMPSGDESIDEKLGLSYKRERPSQAQTEAFWENKQMENNFYKHKSKTKHHSVAEEETLEKHLRPKQKPKNSKHCRDAKFEGTRIPHLVKKRRYQKQDSENKSEAKEQSNDDYVLEKLFKKSVGVHSVMKHDAIMDGASPDYVLVEAEANRVAQDALKALRLSRQRCLGAVSGVPTWTGHRGISGAPAGKKSRFGKKRNSNFSVQHPSSTSPTEKCQDGIMKKEGKDNVPEHFSGRAEDADSSSGPLASSSLLAKMRARNHLILPERLESESGHLQEASALLPTTEHDDLLVEMRNFIAFQAHTDGQASTREILQEFESKLSASQSCVFRELLRNLCTFHRTSGGEGIWKLKPEYC Q03468 Template strand DNA Homo sapiens GATCAAGCTCAAGCGCTCTGCTCCTTCTCCCATCCTCTCGATGGCTATGAGATCAACTAG DNA Non-template strand DNA Homo sapiens LEVO CTAGTTGATCTCATATTTCATTCCTACTCAGGAGAAGGAGCAGAGCGCTTGAGCTTGATC singleParticle particle 0.15 7.5 20.0 HEPES HEPES 100.0 NaCl sodium chloride 2.0 MgCl2 magnesium chloride 10.0 ZnSO4 zinc sulfate 1.0 TCEP tris(2-carboxyethyl)phosphine Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ETHANE 100 277 FEI VITROBOT MARK IV
The final concentration of Pol II is around 0.15 mg/ml. The other components were added in different molar ratio. This sample was glutaraldehyde crosslinked.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.2 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20
Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
GATAN K3 BIOQUANTUM (6k x 4k) 2 13029 3.43 50.0
Two datasets were collected from the same sample using the same parameters.
 1 2866913
Particles were combined from two datasets.
 3.2 FSC 0.143 CUT-OFF cryoSPARC 197558 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_50306.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.019434175 1.7463738 0.00051138195 0.0143760545 1.06 1.06 1.06 0.13 AUTHOR sharpened map emd_50306_msk_1.map emd_50306_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.4399608 0.82406986 -0.00017719093 0.016311532 1.06 1.06 1.06 AUTHOR raw map emd_50306_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.76050806 1.1615529 0.0004946673 0.08588643 1.06 1.06 1.06 AUTHOR half map A emd_50306_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.67016226 1.0706273 0.00049427804 0.086005084 1.06 1.06 1.06 AUTHOR half map B