Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 0
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Widom 601 reverse dna (DNA from synthetic construct)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 1
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Widom 601 reverse dna (DNA from synthetic construct)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 2
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Widom 601 reverse dna (DNA from synthetic construct)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 4
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Widom 601 reverse dna (DNA from synthetic construct)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8to2
Q-score: 0.592
Sauer PV, Cupellini L, Sutter M, Bondanza M, Dominguez Martin MA, Kirst H, Bina D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polivka T, Mennucci B, Kerfeld CA
Sci Adv (2024) 10 pp. eadk7535-eadk7535 [ Pubmed: 38578996 DOI: doi:10.1126/sciadv.adk7535 ]
- Allophycocyanin subunit beta-18 (18 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803)
- Complex of phycobilisome from synechocystis pcc 6803 bound to ocp (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Orange carotenoid-binding protein (34 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycocyanobilin (588 Da, Ligand)
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Translation initiation factor if-2 (12 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin subunit alpha-b (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803)
Structure of the Nucleosome Core Particle from Trypanosoma brucei
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8com
Q-score: 0.439
Deak G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson JA, Tuijtel MW, Webb S, Wilson MD
Nucleic Acids Res (2023) 51 pp. 7882-7899 [ DOI: doi:10.1093/nar/gkad577 Pubmed: 37427792 ]
- Histone octamer (Complex from Trypanosoma brucei brucei TREU927)
- Nucleosome core particle (89 kDa, Complex from Trypanosoma brucei brucei TREU927)
- Histone h2b (12 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Widom 601 145 bp dna (127-mer ordered and built) (44 kDa, DNA from synthetic construct)
- Widom 601 145 bp dna (127-mer ordered and built) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Histone h2a (14 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Widom 601 145 bp dna (Complex from synthetic construct)
- Histone h3, putative (14 kDa, Protein from Trypanosoma brucei brucei TREU927)
Synechocystis PCC 6803 Phycobilisome core from up-down rod conformation
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7sc7
Q-score: 0.454
Dominguez-Martin MA, Sauer PV, Kirst H, Sutter M, Bina D, Greber BJ, Nogales E, Polivka T, Kerfeld CA
Nature (2022) 609 pp. 835-845 [ DOI: doi:10.1038/s41586-022-05156-4 Pubmed: 36045294 ]
- Sll1873 protein (12 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome from synechocystis pcc 6803 (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycocyanobilin (588 Da, Ligand)
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Allophycocyanin subunit beta-18 (18 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Allophycocyanin subunit alpha-b (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
Synechocystis PCC 6803 Phycobilisome rod from PBS sample
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 7sc8
Q-score: 0.598
Dominguez-Martin MA, Sauer PV, Kirst H, Sutter M, Bina D, Greber BJ, Nogales E, Polivka T, Kerfeld CA
Nature (2022) 609 pp. 835-845 [ DOI: doi:10.1038/s41586-022-05156-4 Pubmed: 36045294 ]
- Water (18 Da, Ligand)
- Phycobilisome from synechocystis pcc 6803 (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 1 (32 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- C-phycocyanin alpha subunit (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome 8.9 kda linker polypeptide, phycocyanin-associated, rod (9 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- C-phycocyanin beta subunit (18 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycocyanobilin (588 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 2 (30 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
Synechocystis PCC 6803 Phycobilisome core, complex with OCP
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7sc9
Q-score: 0.449
Dominguez-Martin MA, Sauer PV, Kirst H, Sutter M, Bina D, Greber BJ, Nogales E, Polivka T, Kerfeld CA
Nature (2022) 609 pp. 835-845 [ DOI: doi:10.1038/s41586-022-05156-4 Pubmed: 36045294 ]
- Sll1873 protein (12 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycocyanobilin (588 Da, Ligand)
- Complex of phycobilisome from synechocystis pcc 6803 with ocp (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Allophycocyanin subunit beta-18 (18 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Orange carotenoid-binding protein (34 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Allophycocyanin subunit alpha-b (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
Synechocystis PCC 6803 Phycobilisome rod from OCP-PBS complex sample
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 7sca
Q-score: 0.712
Dominguez-Martin MA, Sauer PV, Kirst H, Sutter M, Bina D, Greber BJ, Nogales E, Polivka T, Kerfeld CA
Nature (2022) 609 pp. 835-845 [ DOI: doi:10.1038/s41586-022-05156-4 Pubmed: 36045294 ]
- Water (18 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 1 (32 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- C-phycocyanin alpha subunit (17 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome 8.9 kda linker polypeptide, phycocyanin-associated, rod (9 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Complex of phycobilisome from synechocystis pcc 6803 with ocp (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- C-phycocyanin beta subunit (18 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycocyanobilin (588 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 2 (30 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803 substr. Kazusa)