Cryo-EM map of Yarrowia lipolytica ORC-Cdc6 bound to 60bp segment of OriA-006 DNA

2026-09-30 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2026-03-11 2026-09-30 2026-09-30 2026-09-30 Howard Hughes Medical Institute (HHMI) United States Cryo-EM map of Yarrowia lipolytica ORC-Cdc6 bound to 60bp segment of OriA-006 DNA Bauer J Joshua-Tor L Origin Recognition Complex, ORC, origin licensing, ATPase, REPLICATION Bauer J Zali N Chouhan OP El Demerdash O Loell K Kinney J Joshua-Tor L Stillman B Evolution of Origin Sequence and Recognition for Licensing of Eukaryotic DNA Replication To Be Published 0353 11su FULLOVERLAP EMDB EMD-76022 associated EM volume

Structure of Yarrowia lipolytica ORC-Cdc6 bound to 60bp segment of OriA-006 DNA

ORC-Cdc6 complex of Yarrowia lipolytica bound to a 60bp DNA segment of OriA-006 ORC-Cdc6 complex of Yarrowia lipolytica bound to a 60bp DNA segment of OriA-006 0 1 2 3 4 5 6 7 8 9

Purified YlORC1-6 was mixed with glycerol-free buffer containing ATP and magnesium acetate, a 60 bp OriA-006 fragment, and YlCdc6 at an ORC:DNA:Cdc6 molar ratio of 1:1.5:4 in a stepwise fashion. Final protein concentration of 1 mg/mL, with 0.05% lauryl maltose neopentyl glycol (LMNG). Blotted using a Leica EM GP2 automatic plunge freezer.

Yarrowia lipolytica 0.4895 Origin recognition complex subunit 1 (Orc1) Yarrowia lipolytica 0.096564922

Contained N-terminal TwinStrep-SUMOstar-TEV tag which was left on to improve solubility of complex during concentration.

1 Spodoptera frugiperda LEVO MSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKTGSLQDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLR RLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGIPTTENLYFQGMTKEYTAIYSPEAKSAP KNKKKAAVRAIRDQDNVEISAGDVVLLKDDPDVEGKEFALIQGLKHGDQGLEAKCVLMKLFNDAEALTPKHVIPNTNKNR YSKGQELVMMNSIVDVLVEELHLPVNCYSFAEFEALSREDKKGDNVYFCRYVFDNDANKTSVEFDWQDITKDMCGFIDIL YELITDKPRKRRAAVKASRQRSRHARDEDESDFELEEEEEEEEEDDIEDIDEDDEYDSPVEQVKKARTPKSAKKNTKKAP ATTPRKRALEDLDLPQPDHNTTPMTTPKKKRKTENGHGLATPKRMFYKQALSDATLPYKTADLSPSKLSPHQSARAKLHV AAVPDTLPCRETEFSNVYLGIESAIRSGSGTCIFVSGTPGSGKTATVREVVSQLQIRVEDNEIPDFLFVELNGMKLTNPH TTYELLWEQLSGERLAYNNAIKLLEHRFQQKSNDTPLVVVLDELDQLVTLNQSVMYNFFNWPTLPHSKLIVVAIANTMDL PERTLSNKISSRLGLTRIQFPGYTHEQLKLIIESRLGDIAESSGTVVRPDAIEFASRKIASVSGDARRALDLCRRAVEIA ELDSEEVQIKHIQQAANEATSTPIYNYLQGLPLAFKIFLCALLARKRRNGLPSDSLGDIIEEIERMIKSSENAGFLSHIL LQGGKRVRMAGFMNAVTELVEAGIIIQQSIKGERSAQVRLTIGVEEITSALKNDDDVKGML Q6C9L7 Origin recognition complex subunit 2 (Orc2) Yarrowia lipolytica 0.057479059 1 Spodoptera frugiperda LEVO MSRRKAPVSYSGLDTSDVSDEDFEVEDEVSTPKRRKTTSPRKQTPRRTASPRKAPGTPSPVKRSLHDKSARKKANRTLLD QSLGLVSEDEDEIELAERIIGESRAPILDSSNDFHTDERSLANVGALIAAEDRVLFLDSSEGYFDQHKTRGRGNANTMAK APAIDHSVFFKYTNQANELFHADQKKMLRHAYRGMFSQWIFELSEGFSLLFYGLGSKRELLTDFVCEKVDSEIPILVING YNASVQFKSVLNSVVDVLYENHEDIFAKKGFVVRNKLPKDVDLLVKLVVDTMRDIEAGSKPSLVVLCHNVDGESLRIDKA STHLSQLMSISQIWFVASVDHIMAPLMWDSAKLASYNFVWHDVTTFAPYTVETSFDDPLLLGKKAEAQGAKGVKYVLESV TPNHRSLYKNLIYCQLEEFHNVADKRKLPEAEVGALTGSTSISVDYDKVLTECLNELTVSNKKDFQEKLKEFMDHKMVVA FDDKMGMKKLYIPFSKDVVQQILEGYLDA Q6C865 Origin recognition complex subunit 3 (Orc3) Yarrowia lipolytica 0.078749531 1 Spodoptera frugiperda LEVO MSNHATLLQREDQKTSYFLSDEIRALKRRRLDKSDPPKNGHKPEIDETNDSGENSETAEREDEKTTLGEIENEGHDNPDE NNPFARLLGGKEPSSGVNLRWNMYQEAWGAQKAKIDELLEMTNGNILEEIVEYVSESDAENQIPAALVFPGSNIANHVRL FGQIREWLGAVKGVHMVTLHARTCPSLKAVIKNIVSDLIESEEVAEEVEVREEDLNYDRRVKYDFSILAEWCRKVGTDAS QRIVLILEDVDSFDVKVLSNLVLMMHSYKDEIPFRLVFGIATSLEIFEHKMTKTSIRHLQGRVFDAQATSMFQSLFENHM FNLNNKSIIVGPTILEDILKRQNVSTESIDAFISSLKYAYMSHYYSNPFSIFTSRLLDAGDEYEQIIDSNLTGEHIDALR MLPSFRALAESKTDASEIDALLSDDSHIMDITKQAVHDFKVTARRVVSLINLFETIENVFGKFPMSWGKTEIYIPLVRGE LGESDFFKAVCESFKSQSDEKIQHLAQELAKDDLFDWLHDPDTILDTITEALHNLKPFKQHLYHEIFVTDLATLQQNVFV PFQRPAIETALADPRHYLGIEDDDNKFKFVDPNISTLFTLYRESGIYINIYDWYVAFKECMPRSVIETELKKQGLVPEEG ETVEDWDKRTLSWFYQAAAELKFIGCVRDTKRKVESVEKLIWRGL Q6C1N4 Origin recognition complex subunit 4 (Orc4) Yarrowia lipolytica 0.05768428899999999 1 Spodoptera frugiperda LEVO MESEFPEIGGEITPTGDEMDVEIVEEVVEPAAPVLPPPQVPKPEAVSETMIDTIKSRTLSILTGKSIPEPIFLDGEKARV YSLMENAIRFGEGNSCIIVGPRGTGKTLIVESALTELEEKYNSAGSQNNFITIRLSGYAQTDDKMAVREIARQLDTVLLN QGQLIENKSISETLNQILSLFDRADIDESEKETVSLVFILDEFDRFCSTTKQTLLYTLFDVAQSSRAPIAVIGLTPRINA RELLEKRVRSRFSQRVVQVKRQHGMNDFWAILRNAVIYPENLLTMVKEEGGNKTALHTDVDLDTVRYWNWHWESMFQAGP LRDHVERLFHTTKSCREFFTSAILAVSQANPWINPNDFVTDVFERGVADTESFIEGLSDLELSLIICAAKVEVMFEVDQV NFNLAYEEYIKTAKEQREALRAVDLEGMATGTVAGFRIWSRGVARAAWEKLESLNLLSPVEKSAKRVAKQLASDTSLDDE IRMTRVDVSLQELTNMLGNSHHLIQWTKIRR Q6C5R0 Origin recognition complex subunit 5 (Orc5) Yarrowia lipolytica 0.052939546999999997 1 Spodoptera frugiperda LEVO MLPKDVVAATRRQVSCRDTQIKLLSVLLSEKAQEMPQSILVHGEPSTGKSTVLKHLLKQSSINHSIILAEQCLTTRILLQ RTFRAVVEDSGKTLADDFEIICENVTAFMALLERFKAQYDFTKPHVIVLDGLDKLHENPSEIYHCFTRLNEMTSIRNVSF IFTISTLEPRALITSSIPHVRFTRYTKEEVVTILSEHELCRLPQTILSEAAKNGTEEEKDVLSRQFWGSYCQVLVDALSP YASSDVSLYKQIARRIWPVYVDPVITGSADMRETAKLYVQSQHIFSSEFAVADSLVQPGMEEALKRKRNNEQDLTGSYDL PLHSKYILVAAYLASYNPERYDIRFFSKQKDGRKGRRDTGRRKRLTLNPRMLEAPPFELERMLAILHSISPEEQFGTAAG VQSMSNIDLPGQIATLTTLKLLVRTSGDPLDSRTKWKVNAGWGLIERLARDIELPIHNYLLDENE Q6CG25 Origin recognition complex subunit 6 (Orc6) Yarrowia lipolytica 0.041218355 1 Spodoptera frugiperda LEVO MNQQINAEIVKLVGNVPIPREVTNLASTLMGKAQTIPMKPNETPARMALCAHVAIEKLLIELQLPAPKQSQPPVPPRSYE KLLQLFREELLGAPPGPSTPRKRKSPMKNPELVAQRTPKTPRTARQVQKDIQESGRSDANVIGEDLLNSEAIGEEDGLLP DTPSKTKKSPQKSPRKGGPKQDDPQPADIEFITKELRFPKHALEGVQRGFDFYWALVKDRWGLLFGLLMTIAFHIQHRSF TDTEATREAFKQRALQLTRRAGMPEDRVEEWIGWTETILKDQMWVKILEQKSGIAPGVIQRQLDRQTSKSSFSGIGNMIP ASFAFNSYRKRNDYHNWKASMLVKMKELKGQEGLEESGTIKVQGE Q6BZQ7 Cell division control protein 6 (Cdc6) Yarrowia lipolytica 0.066907148

Originally contained an N-terminal 8xHis-TEV tag for purification, which was subsequently cleaved using TEV protease. Chains K and L are N-terminal regions of Cdc6.

3 Escherichia coli BL21(DE3) LEVO GMAVATPKRPQKRVRREPIRVPLKELEVNKGEDMGGQQVGEVDRGVSTEPLCLKRRKVECFEDDSVRVLSPPRESCDPFT DSSATSGSSFASPPPLHPHLVELNKIKSMFSRGSKGHILAADQEMVGRQVEEATLLRYFEGRLQAKYSQPGAALYVSGPP GTGKTALLQRVMDKVFRGKEGIKVASINCMLAPSARAIMNLIYKQLSGVEENEALSADISFDKSVAKLEELFMCQTSKEF AERGTSIVVLDEIDHIMTRDQDILFRIFEWAFCKGSRLILVGIANALDLTDRFLPRLKANNFYPQLLKFKPYDAVQIASI IKSRIVKASDEFSREHSSLKKEVVVKKEEDLILSPLNTPKKTQIDPTTLTLTPPHTPTDKTPAVAPTTMAIHPAAIQLCA RKASANTGDLRKAFDICRKALEISEQEFIQKLAQNDPSTVSKPVVSIATMARVCSQVFGGNNSQRIKMLNLQQKAVLCTV ASAEKQLSIEAITSGVDVPLTIQRLFDHYTSSCKKHRMLSPLPFNEFLDVCSALESYSVINITGICGKKNLGINGKGRAS KGGTGASKGEVYGIRDDYVQRKVTLNVQRMDIASAIEVEWLQKYL Q6CDG7 DNA (60-MER) Yarrowia lipolytica 0.018255709 1 (DC)(DT)(DC)(DC)(DA)(DC)(DC)(DC)(DA)(DA)(DT)(DA)(DT)(DG)(DC)(DC)(DC)(DC)(DT)(DC) (DC)(DA)(DA)(DT)(DC)(DC)(DA)(DG)(DC)(DT)(DC)(DC)(DT)(DA)(DC)(DA)(DA)(DG)(DT)(DC) (DG)(DG)(DG)(DG)(DT)(DT)(DG)(DA)(DG)(DA)(DC)(DT)(DG)(DC)(DA)(DC)(DC)(DA)(DA)(DA) DNA DNA (60-MER) Yarrowia lipolytica 0.018730945 1 (DT)(DT)(DT)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DT)(DC)(DT)(DC)(DA)(DA)(DC)(DC)(DC)(DC) (DG)(DA)(DC)(DT)(DT)(DG)(DT)(DA)(DG)(DG)(DA)(DG)(DC)(DT)(DG)(DG)(DA)(DT)(DT)(DG) (DG)(DA)(DG)(DG)(DG)(DG)(DC)(DA)(DT)(DA)(DT)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DA)(DG) DNA MAGNESIUM ION 2.4305e-05 4 MG ADENOSINE-5'-TRIPHOSPHATE 0.000507181 4 ATP water 1.8015e-05 55 HOH singleParticle particle 1 7.5 50.0 HEPES 150.0 KOAc potassium acetate 10.0 MgOAc magnesium acetate 1.0 ATP adenosine triphosphate 1.0 DTT dithiothreitol 0.05 lauryl maltose neopentyl glycol

50 mM HEPES pH 7.5, 150 mM KOAc, 10 mM Mg(OAc)2, 1 mM ATP, 1 mM DTT

EMS Lacey Carbon COPPER 300 CARBON LACEY GLOW DISCHARGE ETHANE 95 298 LEICA EM GP

Sample was applied to a glow-discharged lacey carbon grid and blotted for 3.0 seconds, and plunged into liquid ethane using a Leica Automatic Plunge Freezer EM GP2..

Pre-incubated in assembly buffer (50 mM HEPES pH 7.5, 150 mM KOAc, 10 mM Mg(OAc)2, 1 mM ATP, 1 mM DTT) for 10 minutes.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 8340 78.8

Cryo-electron microscopy data were collected using an FEI/ThermoFisher Titan Krios TEM operating at 300 keV. A Gatan K3 direct electron detector equipped with a BioQuantum energy filter was utilized to semi-automatically collect dose-fractionated movies with ThermoFisher EPU data collection software. For the YlODC60bpOri-A006-WT data collection, a single session was used to collect 8340 exposures, with movies containing 40 frames at a dose rate of 1.97 e/A^2 per frame, totaling 78.8 e/A^2 in cumulative dose.

1 793509

Particle picking used a BoxNet pre-trained neural network implemented in TensorFlow, with a particle diameter of 180 angstrom and a threshold score of 0.4

cryoSPARC 4.7.1 cryoSPARC Patch CTF Refinement and final CTF refinement in the Non-Uniform refinement job provided final CTF estimation/corrections.

CTF correction was done first in WARP during initial screening, and re-corrected in cryoSPARC during the re-picking of particles from micrographs and during the refinements/reconstruction of the map in cryoSPARC

PHASE FLIPPING AND AMPLITUDE CORRECTION

A YlODC54bpOriC-061 map with weak Cdc6 density was imported into the project and heterogeneous refinement with six ab-initio maps and the imported YlODC54bpOriC-061 map was carried out on the entire particle dataset.

2 FOURIER SPACE 2.64 FSC 0.143 CUT-OFF cryoSPARC 4.7.1 Non-uniform refinement was carried out for the final reconstruction.

Non-uniform refinement was used for the final reconstruction.

125267 MAXIMUM LIKELIHOOD cryoSPARC 4.7.1 cryoSPARC heterogeneous refinement was used for initial angular assignment

Starting map was generated from data from previous collection of complex using shorter DNA (45bp OriC-061 vs. 54bp), which started from an ab-initio generated map and underwent multiple refinements and reconstructions, which was then input into a heterogeneous refinement along with other ab-initio classes for the particles/data used in the generation of this map.

MAXIMUM LIKELIHOOD cryoSPARC 4.7.1 Non-uniform refinement was carried out for the final angle assignment.

cryoSPARC non-uniform refinement was used for final angle assignment and refinement

3 82246.0 cryoSPARC 4.7.1 Non-uniform refinement was carried out for the final 3D classification.

Final 3D classification classes consisted of two genuine classes and one class of junk particles. The two genuine classes were combined and further cleanup was done by subsetting particles via per-particle scale.

emd_76022.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 357.264 357.264 357.264 90.0 90.0 90.0 X Y Z -0.08531191 0.28507534 -0.00004780511 0.0061441404 0.827 0.827 0.827 0.05 AUTHOR ::::EMDATABANK.org::::EMD-76022:::: Original unsharpened map Other experimental model

The initial model came from the experimental structure of YlODC54bpOriC-061

FLEXIBLE FIT

The YlODC54bpOriC-061 structure was docked into the map using ChimeraX and used as a starting point, with the DNA sequences substituted and manual refinement in Coot used to build the model.

REAL emd_76022_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 357.264 357.264 357.264 90.0 90.0 90.0 X Y Z -0.44029787 0.7894768 -0.000047805115 0.015426061 0.827 0.827 0.827 AUTHOR ::::EMDATABANK.org::::EMD-76022:::: Sharpened map used to supplement building of structure, sharpened @ B factor = -72.1 emd_76022_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 357.264 357.264 357.264 90.0 90.0 90.0 X Y Z -0.15457575 0.36184672 0.0001807035 0.018773371 0.827 0.827 0.827 AUTHOR ::::EMDATABANK.org::::EMD-76022:::: emd_76022_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 357.264 357.264 357.264 90.0 90.0 90.0 X Y Z -0.15333617 0.37283877 0.00018179347 0.018740108 0.827 0.827 0.827 AUTHOR ::::EMDATABANK.org::::EMD-76022::::