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 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Venette-Smith NL Vishwakarma RK Dollinger R Schultz J Venkatakrishnan V Babitzke P Anand G Gilmour DS Armache J-P Murakami KS polymerase, Pol II, transcription, mRNA Venette-Smith NL Vishwakarma RK Venkatakrishnan V Dollinger R Schultz J Babitzke P Anand G Gilmour DS Armache JP Murakami KS Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster. Nat Commun UK 17 2026 42711332 doi:10.1038/s41467-026-75963-0 2041-1723 EMD-48625 other EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Consensus map
 EMD-48829 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of Pol II
 EMD-48823 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of nucleosome
 EMD-48624 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex
 EMD-48623 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
 EMD-48622 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
 EMD-48621 other EM volume
Structure of native Drosophila melanogaster DLST
 EMD-48620 other EM volume
Structure of a native Drosophila melanogaster hexameric nucleosome
 EMD-48619 other EM volume
Structure of a native Drosophila melanogaster octameric nucleosome
 9mu9 FULLOVERLAP EMDB EMD-48626 associated EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
 EMDB EMD-48625 other EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Consensus map
 EMDB EMD-48829 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of Pol II
 EMDB EMD-48823 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of nucleosome
 EMDB EMD-48624 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex
 EMDB EMD-48623 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
 EMDB EMD-48622 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
 EMDB EMD-48621 other EM volume
Structure of native Drosophila melanogaster DLST
 EMDB EMD-48620 other EM volume
Structure of a native Drosophila melanogaster hexameric nucleosome
 EMDB EMD-48619 other EM volume
Structure of a native Drosophila melanogaster octameric nucleosome
 PDB 9MU9 unspecified
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
 PDB 9MU8 unspecified
Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
 PDB 9MU7 unspecified
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
 PDB 9MU6 unspecified
Structure of native Drosophila melanogaster DLST
 PDB 9MU5 unspecified
Structure of a native Drosophila melanogaster hexameric nucleosome
 PDB 9MU4 unspecified
Structure of a native Drosophila melanogaster octameric nucleosome
 Native purified Nucleosome Elongation Complex from Drosophila melanogaster Native purified Nucleosome Elongation Complex from Drosophila melanogaster 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
A composite structure of a native purified Nucleosome Elongation Complex (Pol II EC - nucleosome)
Drosophila melanogaster 0.750 RNA Drosophila melanogaster 0.0032470999999999997 1 AAAAAAAAAA Template DNA Drosophila melanogaster 0.053243816 1 (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)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) DNA Non-template DNA Drosophila melanogaster 0.050692538999999995 1 (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(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) DNA 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 0.009067585999999999 2 LEVO RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG P84040 DNA-directed RNA polymerase II subunit RPB1 Drosophila melanogaster 0.16642037499999998 1 LEVO SKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDL AKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVMKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPD PNKKPGHGGCGHYQPSIRRTGLDLTAEWKHQNEDSQEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLP VPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGK PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYP GAKYIVRDNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNA DFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWDAKM PQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLH ICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLR QTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDD YGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGED GLCGELVEFQNMPTVKLSNKSFEKRFKFDWSNERLMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQIFPNGE SKVVLPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQANENATLLFQCLIRSTLCTKYV SEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKP KAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPTRISPWLLRI ELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRCIEANMLS DMTLQGIEAIGKVYMHLPQTDSKKRIVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAV RKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGV SENIIMGQLPKMGTGCFDLLLDAEKCRFGI P04052 2.7.7.6 DNA-directed RNA polymerase II subunit RPB2 Drosophila melanogaster 0.132640062 1 LEVO ENAEEISHELWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQI YLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPVETQHQKTFIGKIPIMLRSTYCLLSQLTDRDL TELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDGKYAFKTEIRSCLEHSSRPTSTLWVNMMARGSQNIKKSA IGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGARGARPGVT KDKRIKYAKEILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNL MKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGR DGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNG CWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNY SWQVLVASGVVEYIDTLEEETVMIAMSPYDLKQDKDYAYCTTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGK QAMGVYITNFHVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVF YRSYKDSENKRVGDQEENFEKPHRGTCQGMRNAHYDKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKR DASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMAFTCEGLAPDIIINPH AIPSRMTIGHLIECLQGKLGSNKGEIGDATPFNDAVNVQKISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQR LKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANL RNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVT P08266 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Drosophila melanogaster 0.030676198999999998 1 LEVO PYANQPSVQITELTDDNVKFVLEDTELSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFLAHRIGLIPLISDDVVER LQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSNAKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELK LRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKFFFNVESAGALK PENIVVMGVQVLKNKLSNLQTQLSHESQN O97183 2.7.7.6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Drosophila melanogaster 0.00973651 1 LEVO GGVPKSKRITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYLPDHSYEDWSIDEL IMVD Q24320 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Drosophila melanogaster 0.016946136999999997 1 LEVO AGVLFEDIFNVKDMDPEGKKFDRVSRLHCESESFKMDLILDINSWLYPMELGDKFRLVLATTLREDGCPDSGEYNPMEHE GTRADSFEYVMYGKIYRIEGDEAHNEASRLSAYVSFGGLLMRLQGDANNLHGFEVDQHMYLLMKRLA Q9VNZ3 DNA-directed RNA polymerase II subunit RPB9 Drosophila melanogaster 0.013786585999999998 1 LEVO GFVGIRFCQECNNMLYPKEDKENKILLYACRNCDYKQEADSNCIYVNKIMHEIDELTHIVPDVISDPTLPRTEDHACPKC SHREAVFFQAQTRRAEEEMRLYYVCTNQNCTHRWTE P36958 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Drosophila melanogaster 0.007671124 1 LEVO MIIPIRCFTCGKVIGNKWESYLGLLQAEYTEGDALDALGLKRYCCRRMLLGHVDLIEKLLNYAPLEK Q9VC49 DNA-directed RNA polymerase II subunit RPB11 Drosophila melanogaster 0.01328824 1 LEVO MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAGYKVPHPLEHKFVIRIQTTAD YSPQEAFMNAITDLLAELSLFEERFKDAIKEKKEGG Q9VJE4 DNA-directed RNA polymerase II subunit RPB12 Drosophila melanogaster 0.005647678 1 LEVO TAMTYICGECHHENEMRPRDPIRCRECGYRIMYKKRTKRLVVFDAR Q6IGE3 DNA-directed RNA polymerase II subunit RPB5 Drosophila melanogaster 0.024518331999999997 1 LEVO MDDEAETYKLWRIRKTIMQLSHDRGYLVTQDELDQTLEQFKEMFGDKPSEKRPARSDLIVLVAHNDDPTDQMFVFFPEEP KIGIKTIKTYCTRMQEENIHRAIVVVQGGMTPSAKQSLVDMAPKYILEQFLESELLINITEHELVPEHVVMTVEEKQELL SRYKLKENMLMRIQAGDPVARYFGLKRGQVVKIIRSSETAGRYISYRLVC Q7JZF5 ZINC ION 6.5409e-05 8 ZN 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 ETHANE 100 4 FEI VITROBOT MARK IV
double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes
 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 4197404
Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (4,197,404) is the starting number of particles after initial cleanup and 3D classification of the data representing Pol II and nucleosome subsets, respectively.
 cryoSPARC 4.3.1
'Patch CTF Estimation' in cryoSPARC
PHASE FLIPPING AND AMPLITUDE CORRECTION 'Ab initio' function in cryoSPARC 1 C1 BACK PROJECTION 7.8 FSC 0.143 CUT-OFF cryoSPARC 4.3.1
The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an indvidual focus on the nucleosome and Pol II. This entry represents a composite map of the two locally refined entities.
36552 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1
'Non-Uniform Refinement' in cryoSPARC
 emd_48626.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 Y X Z -0.13090104 0.5718973 0.001082451 0.024066893 1.1538 1.1538 1.1538 0.1 AUTHOR Composite map of the locally refined Pol II and nucleosome from the Nucleosome Elongation Complex. AB INITIO MODEL
The model was based on individual models from this study: octameric nucleosome and Pol II. The models were rigid-body fit into the composite structure, connected and fixed in Coot and Phenix.
50.0 emd_48626_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 Y X Z -0.5048171 0.9849808 0.001082451 0.030950084 1.1538 1.1538 1.1538 AUTHOR Composite map of the locally refined and auto-sharpened Pol II and nucleosome from the Nucleosome Elongation Complex.