9GW2: State 2 MAP 1 SETD2

Name: PDB 9GW2: State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome
Published: 2025-11-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome. Determined by electron microscopy at 4.84 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 4.84 Å
Organisms: synthetic construct, Homo sapiens
Chains: 12
Atoms: 13,114
Mol. weight: 471.44 kDa
Released: 12 Nov 2025

Explore 9GW2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GW2 contains 55 α-helices and 44 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	35-36	2	7
β-strand	37	1	2
α-helix	39-43	5
α-helix	46-57	12
α-helix	65-76	12
β-strand	84-85	2	9
α-helix	87-114	28
β-strand	119-120	2	10
α-helix	122-132	11

Chain b: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	10
α-helix	50-75	26
β-strand	80-81	2	9
α-helix	83-93	11
β-strand	96-98	3	11

Chain c: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	29-36	8
β-strand	43-44	2	12
α-helix	48-73	26
β-strand	78-79	2	13
α-helix	81-90	10
α-helix	92-97	6
β-strand	102-103	2	14

Chain d: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	13
α-helix	56-83	28
β-strand	88-89	2	12
α-helix	91-101	11
α-helix	105-122	18

Chain e: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	46-57	12
α-helix	65-77	13
β-strand	84-85	2	15
α-helix	87-114	28
β-strand	119-120	2	16
α-helix	122-132	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	16
α-helix	50-75	26
β-strand	80-81	2	15
α-helix	83-92	10
β-strand	97-98	2	14

Chain g: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	29-37	9
β-strand	43-44	2	17
α-helix	47-73	27
β-strand	78-79	2	18
α-helix	81-89	9
α-helix	92-97	6
β-strand	101-103	3	11

Chain h: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	18
β-strand	55	1	19
α-helix	56-83	28
β-strand	88-89	2	17
α-helix	91-101	11
α-helix	104-122	19

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	182	synthetic construct
Histone-lysine N-methyltransferase SETD2	O	protein	1133	Homo sapiens	Q9BYW2 (AlphaFold model)
Template DNA	T	DNA	182	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	j	protein	1049	Homo sapiens	Q9Y5B9

Sequence of entity 1 (N), FASTA

>9GW2_1 Non-Template DNA (chains N)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCATCACTGTCGCGGCCCTTGTGTTCAGGAGCCAGCAGGGAGCTGGGA
GC

Sequence of entity 2 (O), FASTA

>9GW2_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

>9GW2_3 Template DNA (chains T)
GCTCCCAGCTCCCTGCTGGCTCCGAGTGGGTTCTGCCGCGACAGTGATGGTGCCGAGGCC
GCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGC
GTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCG
AT

Sequence of entity 4 (a, e), FASTA

>9GW2_4 Histone H3.2 (chains a, e)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVMKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 5 (b, f), FASTA

>9GW2_5 Histone H4 (chains b, f)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (c, g), FASTA

>9GW2_6 Histone H2A type 1-B/E (chains c, g)
SNAPWMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAV
LEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAV
LLPKKTESHHKAKGK

Sequence of entity 7 (d, h), FASTA

>9GW2_7 Histone H2B type 1-K (chains d, h)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 8 (j), FASTA

>9GW2_8 FACT complex subunit SPT16 (chains j)
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…

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