CryoEM structure of canonical rice nucleosome core particle
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8q15
Q-score: 0.401
Hari Sundar G V, Sotelo-Parrilla P, Raju S, Jha S, Gireesh A, Gut F, Vinothkumar KR, Berger F, Jeyaprakash AA, Shivaprasad PV
To Be Published
- Histone h3.2 (15 kDa, Protein from Oryza)
- Widom 601 (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Oryza)
- Widom 601 (44 kDa, DNA from synthetic construct)
- Histone h2a.2 (13 kDa, Protein from Oryza)
- Rice canonical nucleosome core particle with widom 601 dna sequence (Complex from Oryza)
- Histone h2b.4 (16 kDa, Protein from Oryza)
CryoEM structure of rice nucleosome containing a H4 variant chimera
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8q16
Q-score: 0.441
Hari Sundar G V, Sotelo-Parrilla P, Raju S, Jha S, Gireesh A, Gut F, Vinothkumar KR, Berger F, Jeyaprakash AA, Shivaprasad PV
To Be Published
- Rice nucleosome core particle containing a histone h4 variant chimera with widom 601 dna (Complex from Oryza)
- Histone h3.2 (15 kDa, Protein from Oryza)
- Histone h2a.2 (13 kDa, Protein from Oryza)
- Widom 601 (45 kDa, DNA from synthetic construct)
- Widom 601 (45 kDa, DNA from synthetic construct)
- Chimeric h4.v (11 kDa, Protein from Oryza)
- Histone h2b.4 (16 kDa, Protein from Oryza)
Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 9c9w
Q-score: 0.198
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Manganese (ii) ion (54 Da, Ligand)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*ap*gp*ap*tp*cp*ap*gp*ap*ap*tp*gp*ap*ap*tp*ap*tp*ap*cp*tp*ap*ap*a)-3') (7 kDa, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(*ap*tp*tp*gp*gp*ap*gp*tp*tp*cp*ap*tp*gp*tp*gp*ap*tp*gp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (38-mer) (12 kDa, DNA from Homo sapiens)
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Dimerized human top3b-tdrd3 core complexes with a dna mismatch bubble (Complex from Homo sapiens)
Structure of the U11 snRNP core
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9gcm
Q-score: 0.414
Zhao J, Peter D, Brandina I, Liu X, Galej WP
Mol Cell (2025) 85 pp. 652- [ Pubmed: 39809272 DOI: doi:10.1016/j.molcel.2024.12.017 ]
- U11/u12 small nuclear ribonucleoprotein 35 kda protein (29 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 25 kda protein (15 kDa, Protein from Homo sapiens)
- Structure of the u11 snrnp core (130 kDa, Complex from Homo sapiens)
- Programmed cell death protein 7 (54 kDa, Protein from Homo sapiens)
- U11 snrna (43 kDa, RNA from Homo sapiens)
Cryo-EM structure of human core Rab3GAP1/2 complex, local refinement
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8vyb
Q-score: 0.4
Fairlie GMJ, Nguyen KM, Nam SE, Shaw AL, Parson MAH, Shariati HR, Wang X, Jenkins ML, Gong M, Burke JE, Yip CK
Nat Commun (2025) 16 pp. 479-479 [ DOI: doi:10.1038/s41467-025-55828-8 Pubmed: 39779760 ]
- Core rab3gap1/2 complex (Complex from Homo sapiens)
- Rab3gap2 (Complex from Homo sapiens)
- Rab3 gtpase-activating protein non-catalytic subunit (65 kDa, Protein from Homo sapiens)
- Rab3gap1 (Complex from Homo sapiens)
- Isoform 2 of rab3 gtpase-activating protein catalytic subunit (116 kDa, Protein from Homo sapiens)
Structure of the FDX2-bound core ISC complex (proximal conformation)
Resolution: 2.26 Å
EM Method: Single-particle
Fitted PDBs: 8rmc
Q-score: 0.702
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Human fdx2-bound core isc complex (nfs1-isd11-acp1-iscu2-fdx2) (Complex from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
Structure of the FDX2-bound core ISC complex (distal conformation)
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 8rmd
Q-score: 0.642
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Human fdx2-bound core isc complex (nfs1-isd11-acp1-iscu2-fdx2) (Complex from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
Structure of the core ISC complex under turnover conditions (frataxin-bound)
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8rme
Q-score: 0.615
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Frataxin mature form (14 kDa, Protein from Homo sapiens)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
Structure of the core ISC complex under turnover conditions (FDX2-bound in proximal conformation)
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8rmf
Q-score: 0.633
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
Structure of the core ISC complex under turnover conditions (FDX2-bound in distal conformation)
Resolution: 2.46 Å
EM Method: Single-particle
Fitted PDBs: 8rmg
Q-score: 0.598
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)