2026-09-23 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY audit_author citation citation_author em_admin em_author_list _audit_author.name _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update _em_author_list.author EXPERIMENTAL_SUMMARY citation citation_author em_admin em_author_list _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update _em_author_list.author DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update RCSB RCSB 2025-01-13 2025-02-19 2025-02-19 2026-09-23 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM131860 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM047477 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM098399 United States Venette-Smith NL Vishwakarma RK Dollinger R Schultz J Venkatakrishnan V Babitzke P Anand G Gilmour DS Armache J-P Murakami KS Nucleosome, histones, histone, chromatin, DNA, GENE REGULATION Venette-Smith NL Vishwakarma RK Venkatakrishnan V Dollinger R Schultz J Babitzke P Anand G Gilmour DS Armache JP Murakami KS Nat Commun UK 17 2026 42711332 doi:10.1038/s41467-026-75963-0 2041-1723 9mu4 FULLOVERLAP EMDB EMD-48619 associated EM volume

Structure of a native Drosophila melanogaster octameric nucleosome

Natively purified octameric nucleosome from Drosophila melanogaster Natively purified octameric nucleosome from Drosophila melanogaster 0 1 2 3 4 5 6

This entry represents a native octameric nucleosome (i.e. containing two H2A/H2B dimers and two H3/H4 dimers), purified from Drosophila melanogaster embryos

Drosophila melanogaster 240 Histone H2A Drosophila melanogaster 0.011552494 2 LEVO AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL NKLLSGVTIAQGGVLPNIQAVLLPKK P84051 Histone H2B Drosophila melanogaster 0.010979741 2 LEVO KKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAK HAVSEGTKAVTKYTSSK P02283 Histone H3 Drosophila melanogaster 0.01174677 2 LEVO KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAK RVTIMPKDIQLARRIRGERA P02299 Histone H4 Drosophila melanogaster 0.009279875 2 LEVO VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF GG P84040 DNA (164-MER) Drosophila melanogaster 0.050381171999999995 1 (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DG)(DA)(DT) (DA)(DT)(DA)(DT) DNA DNA (164-MER) Drosophila melanogaster 0.050861461000000004 1 (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA) DNA singleParticle particle 1.0 7.5 150.0 NaCl Sodium chloride 10.0 HEPES-HCl HEPES 5.0 Glycerol Glycerol 1.0 EDTA EDTA 350.0 FLAG FLAG peptide

10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor

Quantifoil GOLD 200 GOLD HOLEY GLOW DISCHARGE 10 ETHANE 100 4 FEI VITROBOT MARK IV

double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes. We aimed to purify Pol II in tandem with nucleosomes. The free nucleosomes were co-purified with this sample

TFS TALOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 2.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 4 31103 50.65

Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360

1 1848096

Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (1,848,096) is the starting number of particles after initial cleanup and 3D classification of the data.

cryoSPARC 4.3.1

'Patch CTF Estimation' in cryoSPARC

PHASE FLIPPING AND AMPLITUDE CORRECTION 'Ab initio' function in cryoSPARC 1 C1 BACK PROJECTION 3.29 FSC 0.143 CUT-OFF cryoSPARC 4.3.1

The data was processed using cryoSPARC to 3.34 A from 319,428 particles. It was later post-processed using CryoSieve to select the final number of particles, yielding 3.29 A.

66988 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1

'Non-Uniform Refinement' in cryoSPARC

3LZ0 PDB experimental model P02299 a AlphaFold in silico model P84040 b AlphaFold in silico model P84051 c AlphaFold in silico model P02283 d AlphaFold in silico model P02299 e AlphaFold in silico model P84040 f AlphaFold in silico model P84051 g AlphaFold in silico model P02283 h AlphaFold in silico model AB INITIO MODEL

The model was based on PDB: 3LZ0. First, 3LZ0 was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 models for individual Drosophila melanogaster histones were aligned to their 3LZ0 counterparts, and further optimized in the density using rigid-body fit. Then, in Coot, the models were Real-space refined in conjunction with DNA 601 Widom sequence. The DNA sequence was extended, to fit into the density. For the final model optimization, phenix.real_space_refine was used

50.0 emd_48619_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -1.3680784 4.3987136 0.0058100973 0.052366246 1.1538 1.1538 1.1538 AUTHOR ::::EMDATABANK.org::::EMD-48619:::: Refined, auto-sharpened Coulomb potential density map with Bfactor = -50 emd_48619_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.88438153 3.0297768 0.0007899726 0.07106553 1.1538 1.1538 1.1538 AUTHOR ::::EMDATABANK.org::::EMD-48619:::: Half map 2 from cryoSPARC emd_48619_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.96139723 2.775284 0.00078572246 0.07113719 1.1538 1.1538 1.1538 AUTHOR ::::EMDATABANK.org::::EMD-48619:::: Half map 1 from cryoSPARC