The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 6jyl
Q-score: 0.452
Yan L, Wu H, Li X, Gao N, Chen Z
Nat Struct Mol Biol (2019) 26 pp. 258-266 [ DOI: doi:10.1038/s41594-019-0199-9 Pubmed: 30872815 ]
- Iswi (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (167-mer) (51 kDa, Protein from Escherichia coli K-12)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from Escherichia coli K-12)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Iswi-nucleosome-crosslinked (300 kDa, Complex)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
The complex of ISWI-nucleosome in the ADP.BeF-bound state
Resolution: 3.87 Å
EM Method: Single-particle
Fitted PDBs: 6k1p
Q-score: 0.42
Yan L, Wu H, Li X, Gao N, Chen Z
Nat Struct Mol Biol (2019) 26 pp. 258-266 [ DOI: doi:10.1038/s41594-019-0199-9 Pubmed: 30872815 ]
- Nuleosome (Complex from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from Escherichia coli K-12)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- The complex of iswi-nucleosome in the adp-bef-bound state (300 kDa, Complex)
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
- Isw1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
the crosslinked complex of ISWI-nucleosome in the ADP-bound state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6iro
Q-score: 0.435
Yan L, Wu H, Li X, Gao N, Chen Z
Nat Struct Mol Biol (2019) 26 pp. 258-266 [ DOI: doi:10.1038/s41594-019-0199-9 Pubmed: 30872815 ]
- Histone octamer (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from Escherichia coli K-12)
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- The crosslinked complex of iswi-nucleosome in the adp-bound state (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Isw1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5xlo
Q-score: 0.337
Peng R, Xu Y, Zhu T, Li N, Qi J, Chai Y, Wu M, Zhang X, Shi Y, Wang P, Wang J, Gao N, Gao GF
Cell Res (2017) 27 pp. 853-864 [ Pubmed: 28574055 DOI: doi:10.1038/cr.2017.79 ]
- Acrf1 (Complex)
- Anti-crispr proteins acrf1/2 bound to csy surveillance complex with a 32nt spacer crrna backbone region (400 kDa, Complex from Pseudomonas aeruginosa (strain UCBPP-PA14))
- Crispr-associated protein csy3 (37 kDa, Protein from Pseudomonas aeruginosa (strain UCBPP-PA14))
- Crrna with 32nt spacer sequence (19 kDa, RNA from Pseudomonas aeruginosa)
- Crispr-associated protein csy3 (Complex)
- Crrna with 20nt spacer sequence (Complex)
- Uncharacterized protein acrf1 (8 kDa, Protein from Pseudomonas phage JBD30)
Large subunit of Mycobacterium smegmatis
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 5xym
Q-score: 0.518
Li Z, Ge X, Zhang Y, Zheng L, Sanyal S, Gao N
Protein Cell (2018) 9 pp. 384-388 [ Pubmed: 28875450 DOI: doi:10.1007/s13238-017-0456-9 ]
- 50s ribosomal protein l4 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l25 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l20 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Large subunit of mycobacterium smegmatis ribosome (Complex from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l9 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l27 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l5 (21 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l34 (5 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l35 (7 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 23s rna (1 MDa, RNA from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l18 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l15 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l22 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l14 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l3 (23 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l32 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l28 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l33 2 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l29 (8 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l16 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l21 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Uncharacterized protein bl37 (2 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l13 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l6 (19 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l2 (30 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l19 (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l30 (7 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l36 (4 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l23 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l24 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 50s ribosomal protein l17 (21 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 5s rna (38 kDa, RNA from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Small subunit of Mycobacterium smegmatis ribosome
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 5xyu
Q-score: 0.482
Li Z, Ge X, Zhang Y, Zheng L, Sanyal S, Gao N
Protein Cell (2018) 9 pp. 384-388 [ Pubmed: 28875450 DOI: doi:10.1007/s13238-017-0456-9 ]
- Conserved domain protein (4 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s4 (23 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s8 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s20 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s6 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s12 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s15 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s5 (21 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 16s rna (495 kDa, RNA from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s17 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s3 (30 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s11 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s7 (17 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s16 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s14 type z (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s9 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s13 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s10 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s18 2 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Small subunit of mycobacterium smegmatis ribosome (Complex from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- 30s ribosomal protein s19 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Small subunit of Toxoplasma gondii ribosome
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 5xxu
Q-score: 0.444
Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N
Cell Res (2017) 27 pp. 1275-1288 [ DOI: doi:10.1038/cr.2017.104 Pubmed: 28809395 ]
- Ribosomal protein us14 (6 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us10 (25 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es10 (17 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es7 (22 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us15 (17 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es8 (23 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us17 (18 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es30 (6 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us4 (21 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us12 (15 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es25 (18 kDa, Protein from Toxoplasma gondii)
- 18s rna (576 kDa, RNA from Toxoplasma gondii)
- Ribosomal protein us2 (31 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es1 (29 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us19 (17 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es24 (15 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us11 (16 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es27 (9 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es21 (9 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us13 (17 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es12 (15 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es28 (7 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us3 (26 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us7 (21 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es6 (29 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein el41 (5 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es26 (12 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es19 (18 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us9 (16 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es31 (17 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us8 (14 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es17 (15 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein us5 (29 kDa, Protein from Toxoplasma gondii)
- Ribosomal protein es4 (30 kDa, Protein from Toxoplasma gondii)
- Small subunit of toxoplasma gondii ribosome (Complex from Toxoplasma gondii)
Small subunit of Trichomonas vaginalis ribosome
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 5xyi
Q-score: 0.448
Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N
Cell Res (2017) 27 pp. 1275-1288 [ DOI: doi:10.1038/cr.2017.104 Pubmed: 28809395 ]
- Ribosomal protein s3, putative (24 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s26 (13 kDa, Protein from Trichomonas vaginalis)
- El41 (3 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s13p/s18e, putative (17 kDa, Protein from Trichomonas vaginalis)
- Uncharacterized protein (12 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s6 (24 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s3ae, putative (28 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s4 (28 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s21 (9 kDa, Protein from Trichomonas vaginalis)
- Small subunit of trichomonas vaginalis ribosome (Complex from Trichomonas vaginalis)
- Ribosomal protein l7ae, putative (13 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s29, putative (6 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s7, putative (18 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s30 (6 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s13, putative (17 kDa, Protein from Trichomonas vaginalis)
- Plectin/s10 domain containing protein (16 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s27 (9 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein sa (28 kDa, Protein from Trichomonas vaginalis)
- Uncharacterized protein (7 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s16, putative (15 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s24e, putative (16 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s15a (14 kDa, Protein from Trichomonas vaginalis)
- Uncharacterized protein (30 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s19e, putative (16 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s23, putative (15 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s17-b, putative (14 kDa, Protein from Trichomonas vaginalis)
- 18s (508 kDa, RNA from Trichomonas vaginalis)
- Guanine nucleotide-binding protein beta subunit, putative (37 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s14 (16 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s5-b, putative (21 kDa, Protein from Trichomonas vaginalis)
- 40s ribosomal protein s8 (22 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s19, putative (16 kDa, Protein from Trichomonas vaginalis)
- Uncharacterized protein (21 kDa, Protein from Trichomonas vaginalis)
- Uncharacterized protein (18 kDa, Protein from Trichomonas vaginalis)
- Ribosomal protein s10p/s20e, putative (13 kDa, Protein from Trichomonas vaginalis)