DNA-PKcs, Ku, DNA and LigIV N-BRCT in the NHEJ Long-range synaptic complex
Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y
Nature (2021) 593 pp. 294-298 [ DOI: doi:10.1038/s41586-021-03458-7 Pubmed: 33854234 ]
- Prkdc_human dna-dependent protein kinase catalytic subunit (Protein from Homo sapiens)
- Xrcc6_human x-ray repair cross-complementing protein 6 (Protein from Homo sapiens)
- Xrcc5_human x-ray repair cross-complementing protein 5 (Protein from Homo sapiens)
- Dna (31-mer) (DNA from Homo sapiens)
- Dna (30-mer) (DNA from Homo sapiens)
- Dnapk complex and ligiv n-brct in the long-range synaptic complex of nhej (630 kDa, Complex from Homo sapiens)
- Dnli4_human dna ligase 4 (Protein from Homo sapiens)
XLF, XRCC4 and LigIV C-BRCT in the NHEJ Long-range synaptic complex
Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y
Nature (2021) 593 pp. 294-298 [ DOI: doi:10.1038/s41586-021-03458-7 Pubmed: 33854234 ]
- Nhej1_human non-homologous end-joining factor 1 (Protein from Homo sapiens)
- Xlf, xrcc4 and ligiv c-brct in the nhej long-range synaptic complex (250 kDa, Complex from Homo sapiens)
- Xrcc4_human dna repair protein xrcc4 (Protein from Homo sapiens)
- Dnli4_human dna ligase 4 (Protein from Homo sapiens)
NHEJ Long-range synaptic complex
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7lt3
Q-score: 0.118
Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y
Nature (2021) 593 pp. 294-298 [ DOI: doi:10.1038/s41586-021-03458-7 Pubmed: 33854234 ]
- Long-range synaptic complex of nhej (1 MDa, Complex from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Dna (31-mer) (9 kDa, DNA from Homo sapiens)
- Dna (30-mer) (9 kDa, DNA from Homo sapiens)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Unknown peptide (1 kDa, Protein from Homo sapiens)
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 6uxv
Q-score: 0.322
Han Y, Reyes AA, Malik S, He Y
Nature (2020) 579 pp. 452-455 [ Pubmed: 32188938 DOI: doi:10.1038/s41586-020-2087-1 ]
- Swi/snf chromatin-remodeling complex subunit snf5 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae S288C)
- Unknown protein (1 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swi/snf complex subunit swi3 (93 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (2 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription regulatory protein snf2 (194 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf chromatin-remodeling complex subunit swi1 (148 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf6 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Unknown protein (2 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription regulatory protein snf12 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf global transcription activator complex subunit swp82 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swi/snf body module (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
SWI/SNF nucleosome complex with ADP-BeFx
Resolution: 8.96 Å
EM Method: Single-particle
Fitted PDBs: 6uxw
Q-score: 0.122
Han Y, Reyes AA, Malik S, He Y
Nature (2020) 579 pp. 452-455 [ Pubmed: 32188938 DOI: doi:10.1038/s41586-020-2087-1 ]
- 601 sequence bottom strand (56 kDa, DNA from synthetic construct)
- Swi/snf complex subunit swi3 (93 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf2 (194 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf12 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Water (18 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Swi/snf nucleosome complex with adp-befx (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Swi/snf chromatin-remodeling complex subunit snf5 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Phosphate ion (94 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 601 sequence top strand (61 kDa, DNA from synthetic construct)
- Swi/snf chromatin-remodeling complex subunit swi1 (148 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf6 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Swi/snf global transcription activator complex subunit swp82 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae S288C)
Parainfluenza virus 5 L-P complex
Resolution: 4.38 Å
EM Method: Single-particle
Fitted PDBs: 6v85
Q-score: 0.36
Abdella R, Aggarwal M, Okura T, Lamb RA, He Y
PNAS (2020) 117 pp. 4931-4941 [ Pubmed: 32075920 DOI: doi:10.1073/pnas.1919837117 ]
- Phosphoprotein (42 kDa, Protein from Parainfluenza virus 5 (strain W3))
- Zinc ion (65 Da, Ligand)
- P protein (Complex from Simian virus 5 (strain W3))
- L-p complex (170 kDa, Complex from Simian virus 5 (strain W3))
- L protein (Complex from Simian virus 5 (strain W3))
- Rna-directed rna polymerase l (256 kDa, Protein from Parainfluenza virus 5 (strain W3))
Parainfluenza virus 5 L-P complex with an alternate conformation of the CD-MTase-CTD module
Resolution: 4.63 Å
EM Method: Single-particle
Fitted PDBs: 6v86
Q-score: 0.335
Abdella R, Aggarwal M, Okura T, Lamb RA, He Y
PNAS (2020) 117 pp. 4931-4941 [ Pubmed: 32075920 DOI: doi:10.1073/pnas.1919837117 ]
- Phosphoprotein (42 kDa, Protein from Simian virus 5 (strain W3))
- Rna-directed rna polymerase l (256 kDa, Protein from Simian virus 5 (strain W3))
- Zinc ion (65 Da, Ligand)
- P protein (Complex from Simian virus 5 (strain W3))
- L-p complex (170 kDa, Complex from Simian virus 5 (strain W3))
- L protein (Complex from Simian virus 5 (strain W3))
Negative stain 3D reconstruction of PilU with C1 symmetry
Chlebek JL, Hughes HQ, Ratkiewicz AS, Rayyan R, Wang JC, Herrin BE, Dalia TN, Biais N, Dalia AB
PLoS Genet (2019) 15 pp. e1008448-e1008448 [ DOI: doi:10.1371/journal.pgen.1008448 Pubmed: 31626631 ]
- Pil-u (410 kDa, Complex from Vibrio cholerae)
Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a
Dorsey BW, Huang L, Mondragon A
Nucleic Acids Res (2019) 47 pp. 3765-3783 [ Pubmed: 30759237 DOI: doi:10.1093/nar/gkz079 ]