RecBCD in complex with the phage protein gp5.9
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8b1r
Q-score: 0.502
Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS
eLife (2022) 11 [ DOI: doi:10.7554/eLife.83409 Pubmed: 36533901 ]
- Probable recbcd inhibitor gp5.9 (6 kDa, Protein from Escherichia phage T7)
- Recbcd enzyme subunit recc (128 kDa, Protein from Escherichia coli)
- Complex of gp5.9 bound to recbcd (Complex)
- Probable recbcd inhibitor gp5.9 (Complex from Escherichia phage T7)
- Recbcd enzyme subunit recd (66 kDa, Protein from Escherichia coli)
- Recbcd enzyme subunit recb, recc and recd (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Recbcd enzyme subunit recb (134 kDa, Protein from Escherichia coli)
RecBCD-DNA in complex with the phage protein Abc2
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8b1t
Q-score: 0.463
Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS
eLife (2022) 11 [ DOI: doi:10.7554/eLife.83409 Pubmed: 36533901 ]
- Dna (70-mer) (Complex from synthetic construct)
- Dna (70-mer) (21 kDa, DNA from synthetic construct)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Recbcd enzyme subunit recc (128 kDa, Protein from Escherichia coli)
- Recbcd-abc2-dna complex (Complex)
- Recbcd enzyme subunit recd (66 kDa, Protein from Escherichia coli)
- Recbcd enzyme subunit recb, recc and recd (Complex from Escherichia coli)
- Recbcd enzyme subunit recb (134 kDa, Protein from Escherichia coli)
- Anti-recbcd protein 2 (11 kDa, Protein from Salmonella phage P22)
- Magnesium ion (24 Da, Ligand)
- Anti-recbcd protein 2 (Complex from Salmonella phage P22)
RecBCD-DNA in complex with the phage protein Abc2 and host PpiB
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8b1u
Q-score: 0.387
Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS
eLife (2022) 11 [ DOI: doi:10.7554/eLife.83409 Pubmed: 36533901 ]
- Recbcd enzyme subunits recb, recc and recd (Complex from Escherichia coli)
- Dna (70-mer) (Complex from synthetic construct)
- Dna (70-mer) (21 kDa, DNA from synthetic construct)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Recbcd enzyme subunit recc (128 kDa, Protein from Escherichia coli)
- Recbcd enzyme subunit recd (66 kDa, Protein from Escherichia coli)
- Recbcd-abc2-ppib-dna complex (Complex)
- Recbcd enzyme subunit recb (134 kDa, Protein from Escherichia coli)
- Anti-recbcd protein 2 (11 kDa, Protein from Salmonella phage P22)
- Magnesium ion (24 Da, Ligand)
- Anti-recbcd protein 2 (Complex from Salmonella phage P22)
Mfd-bound E.coli RNA polymerase elongation complex - II state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6x43
Q-score: 0.476
Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
eLife (2021) 10 [ Pubmed: 33480355 DOI: doi:10.7554/eLife.62117 ]
- Transcription-repair-coupling factor (130 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Rna (20-mer) (6 kDa, RNA from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli mfd-rna polymerase elongation complex: state ii (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Mfd-bound E.coli RNA polymerase elongation complex - III state
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6x4w
Q-score: 0.375
Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
eLife (2021) 10 [ Pubmed: 33480355 DOI: doi:10.7554/eLife.62117 ]
- Transcription-repair-coupling factor (130 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna (20-mer) (6 kDa, RNA from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Escherichia coli mfd-rna polymerase elongation complex: state iii (570 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
Mfd-bound E.coli RNA polymerase elongation complex - IV state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6x4y
Q-score: 0.443
Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
eLife (2021) 10 [ Pubmed: 33480355 DOI: doi:10.7554/eLife.62117 ]
- Transcription-repair-coupling factor (130 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Rna (20-mer) (6 kDa, RNA from Escherichia coli)
- Escherichia coli mfd-rna polymerase elongation complex: state iv (570 kDa, Complex from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Mfd-bound E.coli RNA polymerase elongation complex - V state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6x50
Q-score: 0.494
Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
eLife (2021) 10 [ Pubmed: 33480355 DOI: doi:10.7554/eLife.62117 ]
- Transcription-repair-coupling factor (130 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Rna (20-mer) (6 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Escherichia coli mfd-rna polymerase elongation complex: state v (570 kDa, Complex from Escherichia coli)
Cryo-EM structure of human NatB complex
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 6vp9
Q-score: 0.515
Deng S, Pan B, Gottlieb L, Petersson J, Marmorstein R
eLife (2020) 9 [ DOI: doi:10.7554/eLife.57491 Pubmed: 32885784 ]
- N-alpha-acetyltransferase 20 (18 kDa, Protein from Homo sapiens)
- N-alpha-acetyltransferase 20, n-alpha-acetyltransferase 25, natb auxiliary subunit (Complex from Homo sapiens)
- N-alpha-acetyltransferase 25, natb auxiliary subunit (112 kDa, Protein from Homo sapiens)
- Mdvfm peptide (Complex from Escherichia coli)
- Human natb complex (Complex)
- Mdvfm peptide (641 Da, Protein from Escherichia coli K-12)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
Structure of the Bacterial Ribosome at 2 Angstrom Resolution (composite structure)
Resolution: 1.98 Å
EM Method: Single-particle
Fitted PDBs: 7k00
Q-score: 0.677
Watson ZL, Ward FR, Meheust R, Ad O, Schepartz A, Banfield JF, Cate JH
eLife (2020) 9 [ Pubmed: 32924932 DOI: doi:10.7554/eLife.60482 ]
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- E-site trna (589 Da, RNA from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Spermine (202 Da, Ligand)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- A-site trna-val (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome (2 MDa, Complex from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- P-site trna-fmet (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Mrna (9 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- Paromomycin (615 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
Cryo-EM structure of nucleotide-free MsbA reconstituted into peptidiscs, conformation 1
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6uz2
Q-score: 0.342
Angiulli G, Dhupar HS, Suzuki H, Wason IS, Duong Van Hoa F, Walz T
eLife (2020) 9 [ DOI: doi:10.7554/eLife.53530 Pubmed: 32125274 ]