type I-B Cascade bound to a PAM-containing dsDNA target at 3.8 angstrom resolution.
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8h67
Q-score: 0.307
Lu M, Yu C, Zhang Y, Ju W, Ye Z, Hua C, Mao J, Hu C, Yang Z, Xiao Y
Nat Commun (2024) 15 pp. 4126-4126 [ DOI: doi:10.1038/s41467-024-48598-2 Pubmed: 38750051 ]
- Crispr associated protein cas8 (69 kDa, Protein from Synechocystis sp. PCC 6714)
- Crispr associated protein cas7 (33 kDa, Protein from Synechocystis sp. PCC 6714)
- Crispr associated protein cas11b (14 kDa, Protein from Synechocystis sp. PCC 6714)
- Crispr associated protein cas5 (26 kDa, Protein from Synechocystis sp. PCC 6714)
- Target dna (3 kDa, DNA from synthetic construct)
- Cryo-em structure of synechocystis sp. pcc6714 cascade bound to a pam-containing dsdna target at 3.8 angstrom resolution. (Complex from Synechocystis sp. PCC 6714)
- Crispr rna (22 kDa, RNA from synthetic construct)
- Non target dna (2 kDa, DNA from synthetic construct)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ip0
Q-score: 0.326
Lu M, Yu C, Zhang Y, Ju W, Ye Z, Hua C, Mao J, Hu C, Yang Z, Xiao Y
Nat Commun (2024) 15 pp. 4126-4126 [ DOI: doi:10.1038/s41467-024-48598-2 Pubmed: 38750051 ]
- Type i-myxan crispr-associated protein cmx8 (63 kDa, Protein from Synechocystis sp. PCC 6714)
- Cryo-em structure of synechocystis sp. pcc6714 cascade bound to a pam-containing dsdna target presented as full r-loop formed state at 3.6 angstrom resolution (Complex from Synechocystis sp. PCC 6714)
- Type i-myxan crispr-associated protein cas5/cmx5/devs (26 kDa, Protein from Synechocystis sp. PCC 6714)
- Crispr associated protein cas11b (14 kDa, Protein from Synechocystis sp. PCC 6714)
- Fruiting body developmental protein r-like protein (33 kDa, Protein from Synechocystis sp. PCC 6714)
- Dna (5'-d(p*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (3 kDa, DNA from synthetic construct)
- Dna (5'-d(p*tp*cp*cp*ap*tp*gp*tp*tp*tp*ap*tp*cp*ap*cp*c)-3') (4 kDa, DNA from synthetic construct)
- Rna (44-mer) (13 kDa, RNA from synthetic construct)
- Dna (41-mer) (12 kDa, DNA from synthetic construct)
Structure of yeast Ubr1 in complex with Ubc2 and N-degron
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7mex
Q-score: 0.45
Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Nature (2021) 600 pp. 334-338 [ Pubmed: 34789879 DOI: doi:10.1038/s41586-021-04097-8 ]
- Yeast ubr1 in complex with ubc2 and n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-conjugating enzyme e2 2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- N-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin (8 kDa, Protein from Homo sapiens)
Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 7mey
Q-score: 0.407
Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Nature (2021) 600 pp. 334-338 [ Pubmed: 34789879 DOI: doi:10.1038/s41586-021-04097-8 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- 2-(ethylamino)ethane-1-thiol (105 Da, Ligand)
- Yeast ubr1 in complex with ubc2 and monoubiquitinated n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Monoubiquitinated n-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-conjugating enzyme e2 2 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM peptide
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 6ys3
Q-score: 0.568
Schulte L, Reitz J, Mao J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer J, Blackledge M, Glaubitz C, Frangakis A, Schwalbe H
Nat Commun (2020) [ ]
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal (Complex from Escherichia coli BL21(DE3))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BL21(DE3))
- 5s rrna (38 kDa, RNA from Escherichia coli BL21(DE3))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal + gbc secm peptide complex (Complex)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BL21(DE3))
- Gamma-crystallin b (7 kDa, Protein from Bos taurus)
- 23s rrna (942 kDa, RNA from Escherichia coli BL21(DE3))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BL21(DE3))
- Glycine-trna glyt (23 kDa, RNA from Escherichia coli BL21(DE3))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l15 (14 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BL21(DE3))
- Gbc secm peptide complex (Complex from Bos taurus)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BL21(DE3))
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BL21(DE3))
MicroED structure of orthorhombic Vancomycin at 1.2 A resolution
Resolution: 1.2 Å
EM Method: Electron Crystallography
Fitted PDBs: 7c4u
Q-score: 0.803
Fan Q, Li L, Xue H, Zhou H, Zhao L, Liu J, Mao J, Wu S, Zhang S, Wu C, Li X, Zhou X, Wang J
Angew Chem Int Ed Engl (2020) 59 pp. 15141-15146 [ DOI: doi:10.1002/anie.202003922 Pubmed: 32432368 ]
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Vancomycin (Complex from Amycolatopsis orientalis)
- Vancomycin (1 kDa, Protein from Amycolatopsis orientalis)
MicroED structure of anorthic Vancomycin at 1.05 A resolution
Resolution: 1.05 Å
EM Method: Electron Crystallography
Fitted PDBs: 7c4v
Q-score: 0.676
Fan Q, Li L, Xue H, Zhou H, Zhao L, Liu J, Mao J, Wu S, Zhang S, Wu C, Li X, Zhou X, Wang J
Angew Chem Int Ed Engl (2020) 59 pp. 15141-15146 [ DOI: doi:10.1002/anie.202003922 Pubmed: 32432368 ]
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Vancomycin (Complex from Amycolatopsis orientalis)
- Vancomycin (1 kDa, Protein from Amycolatopsis orientalis)
Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptide
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 6qdw
Q-score: 0.541
Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H
Nat Commun (2020) 11 pp. 5569-5569 [ DOI: doi:10.1038/s41467-020-19372-x Pubmed: 33149120 ]
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50 ribosomal subunit (Complex from Escherichia coli BL21(DE3))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal + gbc secm peptide complex (Complex)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- Gamma-crystallin b (7 kDa, Protein from Bos taurus)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 23s rrna (942 kDa, RNA from Escherichia coli BL21(DE3))
- Gbc secm peptide (Complex from Bos taurus)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 5s rrna (38 kDa, RNA from Escherichia coli (strain B / BL21-DE3))
- Glycine-trna glyt (23 kDa, RNA from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain B / BL21-DE3))
- 50s ribosomal protein l15 (14 kDa, Protein from Escherichia coli (strain B / BL21-DE3))