9MU9: Histone H2A

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map. Determined by electron microscopy at 7.8 Å resolution. Released 19 Feb 2025.

Method
Electron microscopy
Resolution
7.8 Å
Organism
Drosophila melanogaster
Chains
21
Atoms
42,423
Mol. weight
615.73 kDa
Ligands
ZN
Released
19 Feb 2025

Explore 9MU9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MU9 contains 200 α-helices and 215 β-strands across 18 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains a and e: 4 helices, 2 β-strands

ElementResiduesLengthSheet
α-helix46-5510
α-helix65-7915
β-strand84-8529
α-helix87-11428
β-strand119110
α-helix122-13211
Chain A: 73 helices, 67 β-strands
ElementResiduesLengthSheet
β-strand11111
β-strand17-18212
β-strand21113
α-helix24-307
β-strand43-44214
β-strand47-48214
α-helix491
β-strand82-90915
α-helix96-1038
β-strand106116
β-strand113116
α-helix120-1289
α-helix133-14311
β-strand149117
α-helix163-1664
α-helix169-1713
β-strand179117
α-helix180-1812
β-strand182-185418
β-strand190-193418
β-strand205-207318
α-helix210-2189
α-helix222-2276
α-helix237-2404
β-strand242-247615
β-strand259119
β-strand261119
α-helix267-28721
α-helix292-31019
α-helix318-3203
β-strand321120
α-helix3221
β-strand327120
α-helix331-3355
α-helix349-3513
β-strand354-361821
β-strand369-372421
α-helix374-3796
β-strand381-385522
α-helix3861
α-helix388-3903
α-helix391-40010
β-strand408-412522
β-strand418-420322
α-helix427-4293
β-strand437-441522
β-strand447-451521
α-helix458-4603
β-strand461-468821
β-strand474-476321
α-helix478-4803
α-helix481-4844
β-strand492-496521
α-helix501-5066
α-helix507-5115
β-strand512121
α-helix514-5163
β-strand518123
β-strand525123
α-helix531-54010
β-strand546-548324
α-helix549-5568
α-helix566-5694
β-strand571-573324
β-strand577-579324
α-helix580-5878
β-strand594-597425
β-strand619-623525
β-strand626-629425
α-helix644-6529
α-helix654-67522
α-helix681-6844
α-helix688-71326
α-helix718-7203
α-helix725-75127
α-helix757-7648
α-helix770-7778
β-strand781-782226
β-strand785127
β-strand788127
α-helix789-7913
α-helix809-8124
β-strand814-815226
α-helix825-84420
α-helix846-85914
β-strand864-865228
β-strand871-872228
β-strand878-880328
α-helix883-8853
β-strand888129
β-strand893-897530
α-helix905-9128
α-helix919-9257
β-strand926131
α-helix928-9369
α-helix940-96122
β-strand968-972530
α-helix975-98511
β-strand994131
α-helix998-101114
α-helix1020-102910
α-helix1031-104010
α-helix1045-10495
α-helix1054-107017
β-strand1072129
α-helix1073-10742
β-strand1078128
α-helix1080-10889
α-helix1090-10923
α-helix1113-11208
β-strand1130-1134532
β-strand1135133
α-helix1137-11404
α-helix1143-115311
β-strand1156134
β-strand1162-1169835
α-helix1173-11753
α-helix1179-118810
β-strand1199-12081035
α-helix1210-12156
α-helix1220-123112
β-strand1235-1239535
β-strand1248-1254735
α-helix1273-128614
β-strand1291134
β-strand1299-1302432
β-strand1311-1314436
β-strand1320-1323436
β-strand1327-1331532
β-strand1344133
β-strand1350-1351232
α-helix1354-13607
α-helix1363-138018
α-helix1387-139711
α-helix1418-14225
α-helix1427-143711
β-strand1440-1441212
α-helix1446-14527
α-helix1459-14613
β-strand1463-1467537
Chain b: 3 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix32-4110
β-strand46110
α-helix51-7626
β-strand81-8229
α-helix84-9310
β-strand97-9933
Chain B: 53 helices, 69 β-strands
ElementResiduesLengthSheet
α-helix14-163
α-helix20-3718
α-helix42-498
α-helix50-556
α-helix56-627
α-helix64-652
β-strand66-67238
β-strand84-941138
β-strand98-100339
β-strand106-108339
α-helix111-1166
β-strand122-1341338
β-strand141-1541438
α-helix169-1746
β-strand186-188340
β-strand191-195540
α-helix1961
β-strand197-201541
α-helix2021
β-strand207-210442
β-strand216-224942
β-strand234-241842
α-helix249-2535
β-strand257-260442
β-strand268-269242
α-helix270-2767
α-helix282-2898
α-helix296-3016
α-helix303-3086
α-helix315-32410
α-helix334-34613
α-helix359-37618
α-helix382-3843
α-helix389-3913
β-strand392-395441
α-helix397-42226
α-helix432-4354
α-helix439-45012
α-helix460-4623
β-strand468-470340
α-helix476-4827
β-strand485-487341
α-helix502-5032
β-strand510143
β-strand525-526241
β-strand527143
β-strand532-533244
α-helix540-54910
β-strand552-553245
α-helix554-5563
α-helix559-5613
β-strand566-570545
β-strand573-578645
α-helix581-59313
β-strand603-607545
β-strand612-616545
β-strand622-628744
β-strand629-630246
β-strand633-634246
α-helix638-6447
α-helix654-6596
β-strand663-667544
α-helix670-6723
β-strand676-677244
α-helix680-6834
β-strand697-698244
α-helix702-7054
α-helix716-7183
α-helix721-73111
β-strand734147
β-strand749-753548
β-strand757149
β-strand761-762250
β-strand778-784751
β-strand796-799451
α-helix800-8056
β-strand810-8191048
β-strand829-831352
β-strand839-840252
α-helix847-8493
β-strand855153
α-helix856-8572
β-strand861-862248
β-strand867-869353
β-strand871-874452
α-helix875-8762
α-helix884-8863
β-strand891-893352
β-strand896-897253
β-strand904-9131048
β-strand919-9291148
β-strand936-938354
β-strand945-946254
β-strand947-951551
α-helix953-9553
β-strand958-959255
β-strand967-969351
α-helix973-9775
α-helix980-99516
α-helix9981
β-strand999-1000250
α-helix1010-10189
β-strand1027-1028251
β-strand1030-1031255
α-helix10371
β-strand1038155
α-helix10391
β-strand1043-1050851
β-strand1051-1052254
β-strand1053147
β-strand1062-1064321
α-helix1090-109910
α-helix1102-11065
α-helix1107-11115
β-strand1115-1121711
β-strand1127111
β-strand1129-1131356
β-strand1136-1138356
β-strand1148-1154711
α-helix1155-116612
β-strand1169113
β-strand1172112
Chain c: 5 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix17-204
α-helix27-359
β-strand42-4324
α-helix46-7227
β-strand77-7825
α-helix80-889
α-helix91-966
β-strand100-10236
Chain C: 11 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand8-14757
β-strand18-24757
α-helix28-3912
β-strand43-551358
α-helix61-699
β-strand73159
α-helix82-843
β-strand99-106858
α-helix1121
β-strand113-116460
α-helix117-1193
β-strand121-122258
β-strand129159
α-helix130-1323
β-strand150-154560
β-strand159-1701258
α-helix175-1773
β-strand180-187857
α-helix201-2033
α-helix205-2073
α-helix219-2213
β-strand229-236857
α-helix242-26726
Chains d and h: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix36-4611
β-strand51-5225
α-helix54-8128
β-strand86-8724
α-helix89-9911
α-helix103-12119
Chain E: 9 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix2-2322
β-strand26-27267
α-helix30-334
α-helix37-437
β-strand47168
β-strand52168
β-strand60-64567
β-strand71-75567
β-strand81-82269
α-helix84-9512
β-strand101-106667
β-strand109-110269
α-helix112-1209
β-strand126-131667
α-helix134-1363
β-strand147-151570
α-helix153-16311
β-strand171-173370
α-helix178-1836
α-helix185-1862
β-strand190-197870
β-strand201-209970

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNARRNA10Drosophila melanogaster
Template DNATDNA174Drosophila melanogaster
Non-template DNANDNA163Drosophila melanogaster
Histone H2Ac, gprotein106Drosophila melanogasterP84051 (AlphaFold model)
Histone H2Bd, hprotein97Drosophila melanogasterP02283 (AlphaFold model)
Histone H3a, eprotein100Drosophila melanogasterP02299 (AlphaFold model)
Histone H4b, fprotein80Drosophila melanogasterP84040 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB1Aprotein1470Drosophila melanogasterP04052
DNA-directed RNA polymerase II subunit RPB2Bprotein1164Drosophila melanogasterP08266
DNA-directed RNA polymerase II subunit RPB3Cprotein269Drosophila melanogasterO97183
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein84Drosophila melanogasterQ24320
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein147Drosophila melanogasterQ9VNZ3

5 more molecules are not listed.

Sequence of entity 1 (R), FASTA
>9MU9_1 RNA (chains R)
AAAAAAAAAA
Sequence of entity 2 (T), FASTA
>9MU9_2 Template DNA (chains T)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTT
Sequence of entity 3 (N), FASTA
>9MU9_3 Non-template DNA (chains N)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACGTGCCTGGAGACTAGGGAGTA
ATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAG
CTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT
Sequence of entity 4 (c, g), FASTA
>9MU9_4 Histone H2A (chains c, g)
AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN
KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKK
Sequence of entity 5 (d, h), FASTA
>9MU9_5 Histone H2B (chains d, h)
KKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRST
ITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sequence of entity 6 (a, e), FASTA
>9MU9_6 Histone H3 (chains a, e)
KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA
SEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 7 (b, f), FASTA
>9MU9_7 Histone H4 (chains b, f)
RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVT
AMDVVYALKRQGRTLYGFGG
Sequence of entity 8 (A), FASTA
>9MU9_8 DNA-directed RNA polymerase II subunit RPB1 (chains A)
SKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTSR
CQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIV
MKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPDPNKKPGHGGCGHYQPSIRRT
GLDLTAEWKHQNEDSQEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLP
VPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHV
ATLVDNDMPGMPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLR
IDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVRDNGERIDLRFHPK
SSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNA
DFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVF
ITREQVMNLLMFLPTWDAKMPQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEED
EGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQT
VINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLR
QTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVE
GKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKT
AETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGEDGLCGELVEFQNMPTVKLSNK
SFEKRFKFDWSNERLMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQIFPNGE
SKVVLPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQAN
ENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQS
LGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKA
KNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPTRISPWLLRI
ELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDE
AVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIVITETGEFKAIGEW
LLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVN
YRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGV
SENIIMGQLPKMGTGCFDLLLDAEKCRFGI
Sequence of entity 9 (B), FASTA
>9MU9_9 DNA-directed RNA polymerase II subunit RPB2 (chains B)
ENAEEISHELWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEA
QHTSGEVETPPRFSLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKT
KNVEGLDPVETQHQKTFIGKIPIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSE
KVLIAQEKMATNTVYVFSMKDGKYAFKTEIRSCLEHSSRPTSTLWVNMMARGSQNIKKSA
IGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVV
QEQNVALNFIGARGARPGVTKDKRIKYAKEILQKEMLPHVGVSDFCETKKAYFLGYMVHR
LLLASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNL
ELAIKTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGR
DGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSME
NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE
IRIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVASGVVEYIDTLEEE
TVMIAMSPYDLKQDKDYAYCTTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGK
QAMGVYITNFHVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQ
EDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQEENFEKPHRGTCQGMRNAHYDKLDD
DGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVDQVMLT
LNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMAFTCEGLAPDIIINPH
AIPSRMTIGHLIECLQGKLGSNKGEIGDATPFNDAVNVQKISTFLQEYGYHLRGNEVMYN
GHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEME
RDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRNNTFECKGCKNKTQISQVR
LPYAAKLLFQELMSMNIAPRLMVT
Sequence of entity 10 (C), FASTA
>9MU9_10 DNA-directed RNA polymerase II subunit RPB3 (chains C)
PYANQPSVQITELTDDNVKFVLEDTELSVANSLRRVFIAETPTLAIDWVQLEANSTVLSD
EFLAHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLK
SSNAKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTA
GVCFEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKFFFNVESAGALK
PENIVVMGVQVLKNKLSNLQTQLSHESQN
Sequence of entity 11 (F), FASTA
>9MU9_11 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
GGVPKSKRITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIP
IIIRRYLPDHSYEDWSIDELIMVD
Sequence of entity 12 (H), FASTA
>9MU9_12 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
AGVLFEDIFNVKDMDPEGKKFDRVSRLHCESESFKMDLILDINSWLYPMELGDKFRLVLA
TTLREDGCPDSGEYNPMEHEGTRADSFEYVMYGKIYRIEGDEAHNEASRLSAYVSFGGLL
MRLQGDANNLHGFEVDQHMYLLMKRLA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn8

Primary citation

Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster. Venette-Smith, N.L., Vishwakarma, R.K., Venkatakrishnan, V. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-75963-0 · PubMed

Other PDB entries of the same protein (UniProt P84051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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