9GMR: SIRT7-H3K36MTUnucleosome complex

SIRT7-H3K36MTUnucleosome complex. Determined by electron microscopy at 2.8 Å resolution. Released 29 Jan 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 11
Atoms: 14,763
Mol. weight: 247.19 kDa
Ligands: ZN, A1IY0
Released: 29 Jan 2025

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

Secondary structure: helices and β-sheets

9GMR contains 51 α-helices and 33 β-strands across 9 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-55	11
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	3

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	28-35	8
β-strand	42-43	2	4
α-helix	47-71	25
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	6

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-123	19

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-55	11
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

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	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	28-35	8
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chain K: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	17-36	20
α-helix	51-53	3
α-helix	55-73	19
α-helix	82-98	17
β-strand	102-106	5	11
α-helix	110-114	5
α-helix	147-156	10
β-strand	163-166	4	11
α-helix	172-176	5
α-helix	180-182	3
β-strand	183-185	3	11
β-strand	192-195	4	12
β-strand	202-205	4	12
β-strand	215	1	13
β-strand	218	1	13
β-strand	233	1	12
α-helix	253-260	8
β-strand	263-267	5	11
α-helix	274-276	3
α-helix	278-281	4
α-helix	291	1
β-strand	292-293	2	11
β-strand	296	1	11
α-helix	304-306	3
β-strand	311	1	11
α-helix	315-326	12
α-helix	340-343	4
β-strand	344	1	12
α-helix	345-348	4
α-helix	352-354	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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 2-A	C, G	protein	129	Homo sapiens	Q6FI13 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	126	Homo sapiens	P06899 (AlphaFold model)
DNA (149-mer)	I	DNA	149	Homo sapiens
DNA (149-mer)	J	DNA	149	Homo sapiens
NAD-dependent protein deacetylase sirtuin-7	K	protein	401	Homo sapiens	Q9NRC8

Sequence of entity 1 (A, E), FASTA

>9GMR_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVCLREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9GMR_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9GMR_3 Histone H2A type 2-A (chains C, G)
SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>9GMR_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>9GMR_5 DNA (149-MER) (chains I)
AGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGC
ACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCA
CGTGTCAGATATATACAAGATCCCCTTAC

Sequence of entity 6 (J), FASTA

>9GMR_6 DNA (149-MER) (chains J)
GTAAGGGGATCTTGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGC
GGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGAC
CAATTGAGCGGCCTCGGCACCGGGATTCT

Sequence of entity 7 (K), FASTA

>9GMR_7 NAD-dependent protein deacetylase sirtuin-7 (chains K)
GMAAGGLSRSERKAAERVRRLREEQQRERLRQVSRILRKAAAERSAEEGRLLAESADLVT
ELQGRSRRREGLKRRQEEVCDDPEELRGKVRELASAVRNAKYLVVYTGAGISTAASIPDY
RGPNGVWTLLQKGRSVSAADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLP
RTAISELHGNMYIEVCTSCVPNREYVRVFDVTERTALHRHQTGRTCHKCGTQLRDTIVHF
GERGTLGQPLNWEAATEAASRADTILCLGSSLKVLKKYPRLWCMTKPPSRRPKLYIVNLQ
WTPKDDWAALKLHGKCDDVMRLLMAELGLEIPAYSRWQDPIFSLATPLRAGEEGSHSRKS
LCRSREEAPPGDRGAPLSSAPILGGWFGRGCTKRTKRKKVT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
A1IY0	[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propyla…	C20 H33 N7 O13 P2 S	1

Primary citation

Structural basis of SIRT7 nucleosome engagement and substrate specificity. Moreno-Yruela, C., Ekundayo, B.E., Foteva, P.N. et al. Nat Commun (2025) 16:1328-1328. DOI 10.1038/s41467-025-56529-y · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

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