Medusavirus Nucleosome Core Particle
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ua7
Q-score: 0.438
Toner CM, Hoitsma NM, Weerawarana S, Luger K
Nat Commun (2024) 15 pp. 9138-9138 [ DOI: doi:10.1038/s41467-024-53364-5 Pubmed: 39443461 ]
- Widom 601 dna strand 1 (63 kDa, DNA from synthetic construct)
- Histone h2b (24 kDa, Protein from Medusavirus)
- Widom 601 dna (Complex from synthetic construct)
- Histone h3 (21 kDa, Protein from Medusavirus)
- Medusavirus nucleosome core particle (Complex)
- Widom 601 dna strand 2 (63 kDa, DNA from synthetic construct)
- Histone h2a (28 kDa, Protein from Medusavirus)
- Histone h4 (14 kDa, Protein from Medusavirus)
- Histone complex (Complex from Medusavirus)
Medusavirus Nucleosome Core Particle Native
Toner CM, Hoitsma NM, Weerawarana S, Luger K
Nat Commun (2024) 15 pp. 9138-9138 [ DOI: doi:10.1038/s41467-024-53364-5 Pubmed: 39443461 ]
- Histone h3 (Protein from Medusavirus medusae)
- Histone h2a (Protein from Medusavirus medusae)
- Widom 601 dna (207 mer) strand 2 (DNA from synthetic construct)
- Widom 601 dna (207 mer) strand 1 (DNA from synthetic construct)
- Widom 601 dna (Complex from synthetic construct)
- Medusavirus nucleosome core particle (Complex)
- Histone h2b (Protein from Medusavirus medusae)
- Histone complex (Complex from Medusavirus)
- Histone h4 (Protein from Medusavirus medusae)
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)
Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 8fvi
Q-score: 0.431
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
Nat Commun (2023) 14 pp. 5241-5241 [ DOI: doi:10.1038/s41467-023-40955-x Pubmed: 37640699 ]
- Dna dc->du-editing enzyme apobec-3h (22 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Virion infectivity factor (21 kDa, Protein from Human immunodeficiency virus 1)
- Elongin-b (11 kDa, Protein from Homo sapiens)
- Hetero-hexameric complex of hiv-1 vif and human apobec3h, cbf-beta, elob, eloc, and cul5 (120 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Rna(5'-r(ap*up*up*up*up*up*up*up*up*u)-3') (3 kDa, RNA from Escherichia coli)
- Rna(5'-r(*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (2 kDa, RNA from Escherichia coli)
- Core-binding factor subunit beta (18 kDa, Protein from Homo sapiens)
- Cullin 5 (36 kDa, Protein from Homo sapiens)
Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8fvj
Q-score: 0.374
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
Nat Commun (2023) 14 pp. 5241-5241 [ DOI: doi:10.1038/s41467-023-40955-x Pubmed: 37640699 ]
- Dimeric form of hiv-1 vif in complex with human cbf-beta, elob, eloc, and cul5 (198 kDa, Complex from Homo sapiens)
- Virion infectivity factor (21 kDa, Protein from Human immunodeficiency virus 1)
- Elongin-b (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Cullin-5 (36 kDa, Protein from Homo sapiens)
- Core-binding factor subunit beta (18 kDa, Protein from Homo sapiens)
HIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
Nat Commun (2023) 14 pp. 5241-5241 [ DOI: doi:10.1038/s41467-023-40955-x Pubmed: 37640699 ]
- Elongin-c (Protein from Homo sapiens)
- Cullin-5 (Protein from Homo sapiens)
- Dna dc->du-editing enzyme apobec-3h (Protein from Homo sapiens)
- Virion infectivity factor (Protein from Human immunodeficiency virus 1)
- Ring-box protein 2 (Protein from Homo sapiens)
- Core-binding factor subunit beta (Protein from Homo sapiens)
- Hetero-heptameric complex of hiv-1 vif and human apobec3h, cbf-beta, elob, eloc, cul5, and rbx2 (Complex from Homo sapiens)
- Elongin-b (Protein from Homo sapiens)