Cryo-EM map of Yarrowia lipolytica ORC-Cdc6 bound to 60bp segment of OriA-006 mutant CNNGGNR 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 mutant CNNGGNR 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 11sv FULLOVERLAP EMDB EMD-76023 associated EM volume

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

ORC-Cdc6 complex of Yarrowia lipolytica bound to a 60bp DNA segment of a mutant of OriA-006 containing the CNNGGNR mutation ORC-Cdc6 complex of Yarrowia lipolytica bound to a 60bp DNA segment of a mutant of OriA-006 containing the CNNGGNR mutation 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 mutant OriA-006 fragment, and YlCdc6 at an ORC:DNA:Cdc6 molar ratio of 1:1.5:6 in a stepwise fashion. Final protein concentration of 1.6 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 (Orc1) Yarrowia lipolytica 0.096564922

Contained N-terminal TwinStrep-SUMOstar-TEV tag which was left on to improve solubility of complex during concentration.,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 0.066850094

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 MAVATPKRPQKRVRREPIRVPLKELEVNKGEDMGGQQVGEVDRGVSTEPLCLKRRKVECFEDDSVRVLSPPRESCDPFTD SSATSGSSFASPPPLHPHLVELNKIKSMFSRGSKGHILAADQEMVGRQVEEATLLRYFEGRLQAKYSQPGAALYVSGPPG TGKTALLQRVMDKVFRGKEGIKVASINCMLAPSARAIMNLIYKQLSGVEENEALSADISFDKSVAKLEELFMCQTSKEFA ERGTSIVVLDEIDHIMTRDQDILFRIFEWAFCKGSRLILVGIANALDLTDRFLPRLKANNFYPQLLKFKPYDAVQIASII KSRIVKASDEFSREHSSLKKEVVVKKEEDLILSPLNTPKKTQIDPTTLTLTPPHTPTDKTPAVAPTTMAIHPAAIQLCAR KASANTGDLRKAFDICRKALEISEQEFIQKLAQNDPSTVSKPVVSIATMARVCSQVFGGNNSQRIKMLNLQQKAVLCTVA SAEKQLSIEAITSGVDVPLTIQRLFDHYTSSCKKHRMLSPLPFNEFLDVCSALESYSVINITGICGKKNLGINGKGRASK GGTGASKGEVYGIRDDYVQRKVTLNVQRMDIASAIEVEWLQKYL Q6CDG7 DNA (60-MER) Yarrowia lipolytica 0.018335758 1 (DC)(DT)(DC)(DC)(DA)(DC)(DC)(DC)(DA)(DA)(DT)(DA)(DT)(DG)(DC)(DC)(DC)(DC)(DT)(DG) (DG)(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 0.018650898 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)(DC) (DC)(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 16 HOH singleParticle particle 1.6 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

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 at 25C and 95% humidity, blotted for 2.7 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 2.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 8428 54.8

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. FYlODC60bpOri-A006-CNNGGNR data collection included 8428 exposures from a single session, with 40 frames per movie, a dose rate of 1.37 e/A^2 per frame, and a cumulative dose of 54.8 e/A^2.

1 2710398

8,428 movies were imported into cryoSPARC and underwent patch motion correction and patch CTF corrections to generate corrected micrographs. Template picking of micrographs commenced using representative 2D class averages of the particles used in the final YlODC60bpOri-A006-WT refinement, resulting in 4,708,382 particles being picked. Micrographs and respective particles were then analyzed using the Micrograph Junk Detector job, and after exposure and particle curation resulted in 2,710,398 particles from 7,330 micrographs. Particles were then extracted with a box size of 432 px and Fourier cropped to 128 px.

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

Patch CTF correction was carried out in cryoSPARC using the default settings, and was optimized during the refinements/reconstruction of the map in cryoSPARC.

PHASE FLIPPING AND AMPLITUDE CORRECTION

The YlODC60bpOriA-006-WT map was imported into the project and heterogeneous refinement with eight ab-initio maps and the imported YlODC60bpOriA-006-WT map was carried out on the entire particle dataset.

1 FOURIER SPACE 2.56 FSC 0.143 CUT-OFF cryoSPARC 4.7.1

Non-uniform refinement was used for the final reconstruction.

51222 MAXIMUM LIKELIHOOD cryoSPARC 4.7.1 cryoSPARC heterogeneous refinement was used for initial angular assignment

cryoSPARC heterogeneous refinement of generated ab initio maps and an imported map of YlODC60bpOriA-006-WT, as described in the startup model section.

MAXIMUM LIKELIHOOD cryoSPARC 4.7.1

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

3 28918.0 cryoSPARC 4.7.1 Non-uniform refinement was carried out for the final reconstruction.

Final 3D classification classes differed between the presence of Cdc6 and the conformation of Orc1-AAA.

emd_76023.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 -0.114714526 0.33958712 -0.00012569709 0.007570897 0.827 0.827 0.827 0.05 AUTHOR ::::EMDATABANK.org::::EMD-76023:::: Unsharpened final EM map Other experimental model

The initial model came from the experimental structure of YlODC60bpOriA-006-WT

FLEXIBLE FIT

The YlODC60bpOriA-006-WT structure was docked into the map using ChimeraX and used as a starting point, with the DNA sequence altered at the mutated sites and manual refinement in Coot used to refine the model.

REAL emd_76023_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 -0.4073622 0.8239658 -0.00012569709 0.017388111 0.827 0.827 0.827 AUTHOR ::::EMDATABANK.org::::EMD-76023:::: Sharpened map used in building of structure emd_76023_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 -0.26784366 0.44895908 0.00010681877 0.031063695 0.827 0.827 0.827 AUTHOR ::::EMDATABANK.org::::EMD-76023:::: emd_76023_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 -0.27094254 0.44645122 0.00010904581 0.030937163 0.827 0.827 0.827 AUTHOR ::::EMDATABANK.org::::EMD-76023::::