Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9j0n
Q-score: 0.316
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*cp*c)-3') (13 kDa, RNA from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0o
Q-score: 0.313
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0p
Q-score: 0.311
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
SIRT7:H3K18DTU nucleosome complex
Carlos MY, Babatunde E, Polina F, Esther S, Dongchun N, Henning S, Beat F
To Be Published
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- K18 structure (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (13 kDa, Protein from Homo sapiens)
- Nad-dependent protein deacetylase sirtuin-7 (45 kDa, Protein from Homo sapiens)
- Dna (148-mer) (45 kDa, DNA from Homo sapiens)
- Dna (148-mer) (45 kDa, DNA from Homo sapiens)
SIRT7-H3K36MTUnucleosome complex
Carlos MY, Babatunde E, Polina F, Esther S, Dongchun N, Henning S, Beat F
To Be Published
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- K36 structure (Complex from Homo sapiens)
- [[(2~{r},3~{a}~{r},5~{r},6~{r},6~{a}~{r})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate (673 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (13 kDa, Protein from Homo sapiens)
- Nad-dependent protein deacetylase sirtuin-7 (45 kDa, Protein from Homo sapiens)
- Dna (149-mer) (45 kDa, DNA from Homo sapiens)
- Dna (149-mer) (46 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA.
Ali-Ahmad A, Mors M, Carrer M, Li X, Bilokapic S, Halic M, Cascella M, Sekulic N
bioRxiv (2025) [ Pubmed: 39803555 DOI: doi:10.1101/2024.12.31.630874 ]
- 2x(cenp-a/h4)2 di-tetrasome assembled on alpha-satellite dna. (200 MDa, Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 147 bp human alpha-satellite dna (45 kDa, DNA from Homo sapiens)
- Histone h3-like centromeric protein a (15 kDa, Protein from Homo sapiens)
- 147 bp alpha-satellite dna (45 kDa, DNA from Homo sapiens)
Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 8yny
Q-score: 0.218
Nagamura R, Kujirai T, Kato J, Shuto Y, Kusakizako T, Hirano H, Endo M, Toki S, Saika H, Kurumizaka H, Nureki O
Nat Commun (2024) 15 pp. 10744-10744 [ DOI: doi:10.1038/s41467-024-54768-z Pubmed: 39737984 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Spcas9-sgrna-nucleosome ternary complex (Complex from Homo sapiens)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Dna (175-mer) (53 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (176-mer) (54 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (17-mer) (5 kDa, DNA from Homo sapiens)
- Rna (97-mer) (31 kDa, RNA from Streptococcus pyogenes)
H3K4me3 nucleosome bound to PRC2_AJ1-450
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8vmn
Q-score: 0.39
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01452-x Pubmed: 39774834 ]
- H3k4me3 nucleosome core particle bound to prc2_aj1-450 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vnv
Q-score: 0.357
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01452-x Pubmed: 39774834 ]
- Protein jumonji (49 kDa, Protein from Homo sapiens)
- Dna (26-mer) (8 kDa, DNA from Homo sapiens)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Isoform 2 of histone-lysine n-methyltransferase ezh2 (85 kDa, Protein from Homo sapiens)
- Rbap48 (47 kDa, Protein from Homo sapiens)
- Eed (50 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Zinc finger protein aebp2 (31 kDa, Protein from Homo sapiens)
- Dna (26-mer) (7 kDa, DNA from Homo sapiens)
- H3k36me3-modified histone h3 (2 kDa, Protein from Homo sapiens)
- Prc2_aj1-450 bound to h3k36me3 modified nucleosome with tail engaged (Complex from Homo sapiens)
H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vo0
Q-score: 0.258
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01452-x Pubmed: 39774834 ]
- Histone h4 (8 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (9 kDa, Protein from Xenopus laevis)
- Histone h4 (8 kDa, Protein from Homo sapiens)
- H3k36me3 modified nucleosome core particle (Complex from Homo sapiens)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (9 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)