2026-02-11 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update PDBe PDBe 2023-09-06 2024-08-14 2024-08-14 2026-02-11 Netherlands Organisation for Scientific Research (NWO) TOP 714.017.003 Netherlands European Molecular Biology Organization (EMBO) ALTF 1159-2019 European Union CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 Lee S-H Sixma TK Ubiquitin ligase, DNA repair, LIGASE Llerena Schiffmacher DA Lee SH Kliza KW Theil AF Akita M Helfricht A Bezstarosti K Gonzalo-Hansen C van Attikum H Verlaan-de Vries M Vertegaal ACO Hoeijmakers JHJ Marteijn JA Lans H Demmers JAA Vermeulen M Sixma TK Ogi T Vermeulen W Pines A The small CRL4 CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics. Nat Commun UK 15 6374 6374 2024 39075067 doi:10.1038/s41467-024-50584-7 2041-1723 EMD-18377 focused EM volume
Focused on CSA-DDB1-DDA1 (map 1)
 EMD-18378 focused EM volume
Focused on CSA-DDB1-DDA1 (map 2)
 EMD-18380 focused EM volume
Focused on UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 (map 3)
 EMD-18413 consensus EM volume 8qh5 FULLOVERLAP EMDB EMD-18377 focused EM volume
Focused on CSA-DDB1-DDA1 (map 1)
 EMDB EMD-18378 focused EM volume
Focused on CSA-DDB1-DDA1 (map 2)
 EMDB EMD-18380 focused EM volume
Focused on UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 (map 3)
 EMDB EMD-18398 associated EM volume
CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 - Composite Map
 EMDB EMD-18413 consensus EM volume Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1 Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1 0 2 3 4 1
Ternary complex of ubiquitinated UVSSA-USP7-CSA-DDB1-DDA1. USP7 is invisible in the cryoEM map.
Homo sapiens 0.21 UV-stimulated scaffold protein A Homo sapiens 0.082923164
The construct contains an N-terminal His tag.
1 Spodoptera frugiperda LEVO MAHHHHHHSAALEVLFQGPGMDQKLSKLVEELTTSGEPRLNPEKMKELKKICKSSEEQLSRAYRLLIAQLTQEHAEIRLS AFQIVEELFVRSHQFRMLVVSNFQEFLELTLGTDPAQPLPPPREAAQRLRQATTRAVEGWNEKFGEAYKKLALGYHFLRH NKKVDFQDTNARSLAERKREEEKQKHLDKIYQERASQAEREMQEMSGEIESCLTEVESCFRLLVPFDFDPNPETESLGMA SGMSDALRSSCAGQVGPCRSGTPDPRDGEQPCCSRDLPASAGHPRAGGGAQPSQTATGDPSDEDEDSDLEEFVRSHGLGS HKYTLDVELCSEGLKVQENEDNLALIHAARDTLKLIRNKFLPAVCSWIQRFTRVGTHGGCLKRAIDLKAELELVLRKYKE LDIEPEGGERRRTEALGDAEEDEDDEDFVEVPEKEGYEPHIPDHLRPEYGLEAAPEKDTVVRCLRTRTRMDEEVSDPTSA AAQLRQLRDHLPPPSSASPSRALPEPQEAQKLAAERARAPVVPYGVDLHYWGQELPTAGKIVKSDSQHRFWKPSEVEEEV VNADISEMLRSRHITFAGKFEPVQHWCRAPRPDGRLCERQDRLKCPFHGKIVPRDDEGRPLDPEDRAREQRRQLQKQERP EWQDPELMRDVEAATGQDLGSSRYSGKGRGKKRRYPSLTNLKAQADTARARIGRKVFAKAAVRRVVAAMNRMDQKKHEKF SNQFNYALN Q2YD98 DNA excision repair protein ERCC-8 Homo sapiens 0.045465612999999995
The construct contains a Strep tag II at the C-terminus
1 Spodoptera frugiperda LEVO MLGFLSARQTGLEDPLRLRRAESTRRVLGLELNKDRDVERIHGGGINTLDIEPVEGRYMLSGGSDGVIVLYDLENSSRQS YYTCKAVCSIGRDHPDVHRYSVETVQWYPHDTGMFTSSSFDKTLKVWDTNTLQTADVFNFEETVYSHHMSPVSTKHCLVA VGTRGPKVQLCDLKSGSCSHILQGHRQEILAVSWSPRYDYILATASADSRVKLWDVRRASGCLITLDQHNGKKSQAVESA NTAHNGKVNGLCFTSDGLHLLTVGTDNRMRLWNSSNGENTLVNYGKVCNNSKKGLKFTVSCGCSSEFVFVPYGSTIAVYT VYSGEQITMLKGHYKTVDCCVFQSNFQELYSGSRDCNILAWVPSLYEPVPDDDETTTKSQLNPAFEDAWSSSDEEGGTSA WSHPQFEK Q13216 DNA damage-binding protein 1 Homo sapiens 0.12929886699999998
The construct contains an N-terminal His tag.
1 Spodoptera frugiperda LEVO MAHHHHHHSAALEVLFQGPGMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLF KVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVI AVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSG AFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFC GNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIET GLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLT IGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQT VAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEG NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDI SRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 DET1- and DDB1-associated protein 1 Homo sapiens 0.016997615
The construct contains a TwinStrep tag and a Flag tag at the C-terminus.
1 Spodoptera frugiperda LEVO MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELE GESSAPPRKVARTDSPDMHEDTDVLFQGPGAWSHPQFEKGGGSGGGSGGGSWSHPQFEKGASGEDYKDDDDK Q9BW61 singleParticle particle 0.13 7.5 20.0 HEPES HEPES 150.0 NaCl sodium chloride 0.5 TCEP tris(2-carboxyethyl)phosphine Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE
The grid was coated with graphene oxide.
 ETHANE 100 277 FEI VITROBOT MARK IV
This sample was glutaraldehyde crosslinked
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 3.0 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) 1 1382 60.0 1 723908 cryoSPARC RELION PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.4 FSC 0.143 CUT-OFF RELION 3.3.3
Combined from focused maps reconstructed with various particle numbers.
294142 MAXIMUM LIKELIHOOD cryoSPARC RELION 3.1.3 MAXIMUM LIKELIHOOD RELION 3.1.3 emd_18398.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 338.24 338.24 338.24 90.0 90.0 90.0 Z Y X -1.8985326 85.661789999999996 0.0013382172 0.94812536 1.0569999 1.0569999 1.0569999 0.828 AUTHOR Composite map of UVSSA(VHS)-CSA-DDB1-DDA1 7OO3 P 1-396 PDB experimental model
CSA
 7OO3 T 1-1140 PDB experimental model
DDB1(BPA/BPC)
 6ZX9 A 393-709 PDB experimental model
DDB1(BPB)
 6UD7 D 4-76 PDB experimental model
DDA1
 Q2YD98 A 1-150 AlphaFold in silico model
UVSSA(VHS)
 RIGID BODY FIT
Additional densities are observed near several cysteine residues (A/Cys222, A/Cys260, A/Cys288, B/Cys363, B/Cys725, B/Cys1008). We expect these are oxidized products or crosslinking side products.
REAL