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 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 To Be Published 0353 11st FULLOVERLAP EMDB EMD-76021 associated EM volume

Structure of Yarrowia lipolytica ORC-Cdc6 bound to 54bp segment of OriC-061 DNA

ORC-Cdc6 complex of Yarrowia lipolytica bound to a 54bp DNA segment of OriC-061 ORC-Cdc6 complex of Yarrowia lipolytica bound to a 54bp DNA segment of OriC-061 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 54 bp OriC-061 fragment, and YlCdc6 at an ORC:DNA:Cdc6 molar ratio of 1:1.5:4 in a stepwise fashion, followed by gel filtration. Final protein concentration of 1-1.25 mg/mL, with 0.05% lauryl maltose neopentyl glycol (LMNG). Blotted using a Leica EM GP2 automatic plunge freezer.

Yarrowia lipolytica 0.384 Origin recognition complex subunit 1 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 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

Author provided reference is GenBank XP_504002.3

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. A leftover glycine (residue 0) can be seen in the map. 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 (54-MER) Yarrowia lipolytica 0.01655168 1 (DT)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DA)(DT)(DC)(DC)(DC)(DA)(DA)(DT)(DA)(DT)(DT)(DA) (DC)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DT)(DA)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DA)(DA) (DG)(DC)(DT)(DA)(DA)(DA)(DA)(DG)(DT)(DA)(DA)(DC)(DT)(DC) DNA DNA (54-MER) Yarrowia lipolytica 0.016719715 1 (DG)(DA)(DG)(DT)(DT)(DA)(DC)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DT)(DT)(DA)(DT)(DG)(DC) (DA)(DT)(DG)(DC)(DT)(DA)(DC)(DT)(DT)(DG)(DG)(DG)(DT)(DG)(DT)(DA)(DA)(DT)(DA)(DT) (DT)(DG)(DG)(DG)(DA)(DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DA) DNA MAGNESIUM ION 2.4305e-05 3 MG ADENOSINE-5'-TRIPHOSPHATE 0.000507181 3 ATP ADENOSINE-5'-DIPHOSPHATE 0.000427201 1 ADP water 1.8015e-05 22 HOH singleParticle particle 1.2 7.5 25.0 HEPES 100.0 NaCl sodium chloride 1.0 dithiothreitol 0.05 lauryl maltose neopentyl glycol

25 mM HEPES pH 7.5, 100 mM NaCl, 1 mM DTT, 0.05% LMNG

Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY

ethyl acetate wash

ETHANE 95 298 LEICA EM GP

Sample was applied to a non-glow discharged Quantifoil R 1.2/1.3 300 mesh copper grid (previously washed with ethyl acetate), incubated for 10 seconds, blotted for 2.9 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, 10% glycerol) for 10 minutes before size exclusion chromatography.

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) 3 20341 43.2

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 YlODC54bpOriC-061 data collection, 30-frame movies were collected over three consecutive days, resulting in 9309, 8758, and 2274 exposures taken, respectively, at a dose rate of 1.44 e/A^2 per frame, totaling a cumulative dose of 43.2 e/A^2.

1 3805196

Particle picking used a BoxNet pre-trained neural network implemented in TensorFlow, with a particle diameter of 180 angstrom and a threshold score of 0.5

CTF correction was done first in WARP during exposure/micrograph pre-processing, and re-corrected during the final refinements/reconstruction of the map in cryoSPARC

PHASE FLIPPING AND AMPLITUDE CORRECTION

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.

1 FOURIER SPACE 2.73 FSC 0.143 CUT-OFF cryoSPARC 4.7

Non-uniform refinement was used for the final reconstruction.

51599 MAXIMUM LIKELIHOOD

cryoSPARC heterogeneous refinement of generated ab initio maps and an imported map from the 45bp OriC-061 ODC map refinement, as described in the startup model section.

MAXIMUM LIKELIHOOD

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

2 60002.0

Final 3D classification classes differed between whether or not Cdc6 was visible. Further cleanup on the chosen class was done by subsetting particles via per-particle scale.

AlphaFold in silico model Other in silico model

Generic B-DNA used as template, generated in Coot.

FLEXIBLE FIT

AlphaFold 2 models for each subunit were docked into the density individually using the "fit to map" functionality in ChimeraX, then refined using Coot. The density for the DNA was sharp enough to allow us to discern purines and pyrimidines, allowing us to produce a generic DNA-B form model of the respective DNA sequence and manually rebuild it in Coot. PHENIX Real Space Refine functionality was used to further process and finalize the structure.

REAL emd_76021_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 382.36002 382.36002 382.36002 90.0 90.0 90.0 X Y Z -0.77752984 1.5720016 0.00014268323 0.034888174 0.869 0.869 0.869 AUTHOR ::::EMDATABANK.org::::EMD-76021:::: Cryo-EM sharpened map of the Yarrowia lipolytica ORC-DNA-Cdc6 (ODC) complex with a 54bp dsDNA segment containing part of OriC-061. Used for model building. emd_76021_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 382.36002 382.36002 382.36002 90.0 90.0 90.0 X Y Z -0.8152111 1.1879224 0.0005539961 0.094084874 0.869 0.869 0.869 AUTHOR ::::EMDATABANK.org::::EMD-76021:::: Cryo-EM half map A of the Yarrowia lipolytica ORC-DNA-Cdc6 (ODC) complex with a 54bp dsDNA segment containing part of OriC-061. emd_76021_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 382.36002 382.36002 382.36002 90.0 90.0 90.0 X Y Z -0.73651975 1.2398198 0.0005438922 0.093801744 0.869 0.869 0.869 AUTHOR ::::EMDATABANK.org::::EMD-76021:::: Cryo-EM half map B of the Yarrowia lipolytica ORC-DNA-Cdc6 (ODC) complex with a 54bp dsDNA segment containing part of OriC-061.