9RZC: State 3 MAP 1 SETD2

Name: PDB 9RZC: State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome
Published: 2025-09-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome. Determined by electron microscopy at 3.66 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 3.66 Å
Organisms: synthetic construct, Homo sapiens
Chains: 12
Atoms: 13,235
Mol. weight: 480.71 kDa
Released: 24 Sept 2025

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

Secondary structure: helices and β-sheets

9RZC contains 52 α-helices and 43 β-strands across 10 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.

Chain a: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	1
α-helix	38-42	5
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-112	27
α-helix	113-115	3
β-strand	118-119	2	8
α-helix	121-131	11

Chain b: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	82	1
α-helix	83-92	10
β-strand	96-98	3	9

Chain c: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	10
α-helix	46-72	27
β-strand	77-78	2	11
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	12

Chain d: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	11
α-helix	56-84	29
β-strand	88-89	2	10
α-helix	91-101	11
α-helix	104-122	19

Chain e: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	14
α-helix	86-113	28
β-strand	118-119	2	13
α-helix	121-131	11

Chain f: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	13
α-helix	50-75	26
β-strand	80-81	2	14
α-helix	83-92	10
β-strand	97-98	2	12

Chain g: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	15
α-helix	46-72	27
β-strand	77-78	2	16
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	9
α-helix	113-115	3

Chain h: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	16
β-strand	55	1	17
α-helix	56-83	28
β-strand	88-89	2	15
α-helix	91-101	11
α-helix	104-121	18

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-template DNA	N	DNA	197	synthetic construct
Histone-lysine N-methyltransferase SETD2	O	protein	1133	Homo sapiens	Q9BYW2 (AlphaFold model)
Template DNA	T	DNA	197	synthetic construct
Histone H3.2	a, e	protein	136	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	b, f	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	c, g	protein	135	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	d, h	protein	126	Homo sapiens	O60814
FACT complex subunit SPT16	k	protein	1049	Homo sapiens	Q9Y5B9

Sequence of entity 1 (N), FASTA

>9RZC_1 Non-template DNA (chains N)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGATATCGATCACTGTCGCGGCCCTTGTGTTCAGGAGCC
AGCAGGGAGCTGGGAGC

Sequence of entity 2 (O), FASTA

>9RZC_2 Histone-lysine N-methyltransferase SETD2 (chains O)
SNAETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSH
RDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHAD
VEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKN
DEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRY
GKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRKKDSVDGELEALMENGEGLSD
KNQVLSLSRLMVRIETLEQKLTCLELIQNTHSQSCLKSFLERHGLSLLWIWMAELGDGRE
SNQKLQEEIIKTLEHLPIPTKNMLEESKVLPIIQRWSQTKTAVPPLSEGDGYSSENTSRA
HTPLNTPDPSTKLSTEADTDTPKKLMFRRLKIISENSMDSAISDATSELEGKDGKEDLDQ
LENVPVEEEEELQSQQLLPQQLPECKVDSETNIEASKLPTSEPEADAEIELKESNGTKLE
EPINEETPSQDEEEGVSDVESERSQEQPDKTVDISDLATKLLDSWKDLKEVYRIPKKSQT
EKENTTTERGRDAVGFRDQTPAPKTPNRSRERDPDKQTQNKEKRKRRSSLSPPSSAYERG
TKRPDDRYDTPTSKKKVRIKDRNKLSTEERRKLFEQEVAQREAQKQQQQMQNLGMTSPLP
YDSLGYNAPHHPFAGYPPGYPMQAYVDPSNPNAGKVLLPTPSMDPVCSPAPYDHAQPLVG
HSTEPLSAPPPVPVVPHVAAPVEVSSSQYVAQSDGVVHQDSSVAVLPVPAPGPVQGQNYS
VWDSNQQSVSVQQQYSPAQSQATIYYQGQTCPTVYGVTSPYSQTTPPIVQSYAQPSLQYI
QGQQIFTAHPQGVVVQPAAAVTTIVAPGQPQPLQPSEMVVTNNLLDLPPPSPPKPKTIVL
PPNWKTARDPEGKIYYYHVITRQTQWDPPTWESPGDDASLEHEAEMDLGTPTYDENPMKA
SKKPKTAEADTSSELAKKSKEVFRKEMSQFIVQCLNPYRKPDCKVGRITTTEDFKHLARK
LTHGVMNKELKYCKNPEDLECNENVKHKTKEYIKKYMQKFGAVYKPKEDTELE

Sequence of entity 3 (T), FASTA

>9RZC_3 Template DNA (chains T)
GCTCCCAGCTCCCTGCTGGCTCCGAGTGGGTTCTGCCGCGACAGTGATCGATATCAGAAT
CCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTA
CGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGT
CAGATATATACATCGAT

Sequence of entity 4 (a, e), FASTA

>9RZC_4 Histone H3.2 (chains a, e)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVMKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 5 (b, f), FASTA

>9RZC_5 Histone H4 (chains b, f)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (c, g), FASTA

>9RZC_6 Histone H2A type 1-B/E (chains c, g)
SNAPWMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAV
LEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAV
LLPKKTESHHKAKGK

Sequence of entity 7 (d, h), FASTA

>9RZC_7 Histone H2B type 1-K (chains d, h)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 8 (k), FASTA

>9RZC_8 FACT complex subunit SPT16 (chains k)
SNMAVTLDKDAYYRRVKRLYSNWRKGEDEYANVDAIVVSVGVDEEIVYAKSTALQTWLFG
YELTDTIMVFCDDKIIFMASKKKVEFLKQIANTKGNENANGAPAITLLIREKNESNKSSF
DKMIEAIKESKNGKKIGVFSKDKFPGEFMKSWNDCLNKEGFDKIDISAVVAYTIAVKEDG
ELNLMKKAASITSEVFNKFFKERVMEIVDADEKVRHSKLAESVEKAIEEKKYLAGADPST
VEMCYPPIIQSGGNYNLKFSVVSDKNHMHFGAITCAMGIRFKSYCSNLVRTLMVDPSQEV
QENYNFLLQLQEELLKELRHGVKICDVYNAVMDVVKKQKPELLNKITKNLGFGMGIEFRE
GSLVINSKNQYKLKKGMVFSINLGFSDLTNKEGKKPEEKTYALFIGDTVLVDEDGPATVL
TSVKKKVKNVGIFLKNEDEEEEEEEKDEAEDLLGRGSRAALLTERTRNEMTAEEKRRAHQ
KELAAQLNEEAKRRLTEQKGEQQIQKARKSNVSYKNPSLMPKEPHIREMKIYIDKKYETV
IMPVFGIATPFHIATIKNISMSVEGDYTYLRINFYCPGSALGRNEGNIFPNPEATFVKEI
TYRASNIKAPGEQTVPALNLQNAFRIIKEVQKRYKTREAEEKEKEGIVKQDSLVINLNRS
NPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGDKVDILYNNIKHALFQPCDGEMII
VLHFHLKNAIMFGKKRHTDVQFYTEVGEITTDLGKHQHMHDRDDLYAEQMEREMRHKLKT
AFKNFIEKVEALTKEELEFEVPFRDLGFNGAPYRSTCLLQPTSSALVNATEWPPFVVTLD
EVELIHFERVQFHLKNFDMVIVYKDYSKKVTMINAIPVASLDPIKEWLNSCDLKYTEGVQ
SLNWTKIMKTIVDDPEGFFEQGGWSFLEPEGEGSDAEEGDSESEIEDETFNPSEDDYEEE
EEDSDEDYSSEAEESDYSKESLGSEEESGKDWDELEEEARKADRESRYEEEEEQSRSMSR
KRKASVHSSGRGSNRGSRHSSAPPKKKRK

Primary citation

Molecular mechanism of co-transcriptional H3K36 methylation by SETD2. Walshe, J.L., Ochmann, M., Neef, U. et al. Nat Commun (2025) 16:9565-9565. DOI 10.1038/s41467-025-65439-y · PubMed

Other PDB entries of the same protein (UniProt Q9BYW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
5LT7 1.51 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LT8 1.57 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVS 1.6 Å, Crystal structure of hnRNP LL RRM2 in complex with SETD2
5LSY 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LSZ 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
6J9J 1.78 Å, crystal structure of SESTD2 in complex with H3.3S31phK36M peptide
5LSS 1.79 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVR 1.8 Å, Crystal structure of hnRNP L RRM2 in complex with SETD2
7LZD 1.8 Å, Crystal Structure of SETD2 bound to Compound 35
8Q5P 1.81 Å, Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from…

Browse structure collections

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