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The cryo-EM structure of the EcBAM/EspP(beta8-12) complex
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8sqa
Q-score: 0.408
Wu R, Ryoo D, Kuo KM, Gumbart JC, Noinaj N
To Be Published
- Outer membrane protein assembly factor bamd (25 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamc (34 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamb (39 kDa, Protein from Escherichia coli)
- Maltose/maltodextrin-binding periplasmic protein,autotransporter protein espp translocator (60 kDa, Protein from Escherichia coli O157)
- Outer membrane protein assembly factor bama (88 kDa, Protein from Escherichia coli)
- Bam/espp(beta1-12) (Complex from Escherichia coli)
- Outer membrane protein assembly factor bame (10 kDa, Protein from Escherichia coli)
Resolution: 4.16 Å
EM Method: Single-particle
Fitted PDBs: 9bei
Q-score: 0.276
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PE, Georgeon S, Rosset S, Kapoor S, Choudhury J, Deuparea J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE
To Be Published
- Synthetic human claudin-4 complex with clostridium perfringens enterotoxin c-terminal domain, sfab cop-2, and nanobody against cop-2 (103 kDa, Complex from Homo sapiens)
- Cop-2 fab light chain (23 kDa, Protein from Escherichia coli)
- Cop-2 fab heavy chain (25 kDa, Protein from Escherichia coli)
- Heat-labile enterotoxin b chain (14 kDa, Protein from Clostridium perfringens)
- Claudin-4 (22 kDa, Protein from Homo sapiens)
- Anti-fab nanobody (13 kDa, Protein from Escherichia coli)
Resolution: 4.36 Å
EM Method: Single-particle
Fitted PDBs: 8xbx
Q-score: 0.072
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (5'-d(p*ap*ap*cp*gp*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*cp*cp*ap*cp*g)-3') (48 kDa, DNA from synthetic construct)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*gp*tp*gp*gp*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*cp*gp*tp*t)-3') (48 kDa, DNA from Escherichia coli)
- Rad51-nucleosome complex (Complex from Homo sapiens)
Escherichia coli paused disome complex (Rotated disome interface class 1)
Resolution: 4.46 Å
EM Method: Single-particle
Fitted PDBs: 8rcs
Q-score: 0.218
Flugel T, Schacherl M, Unbehaun A, Schroeer B, Dabrowski M, Burger J, Mielke T, Sprink T, Diebolder CA, Guillen Schlippe YV, Spahn CMT
Nat Commun (2024) 15 pp. 1756-1756 [ DOI: doi:10.1038/s41467-024-46092-3 Pubmed: 38409277 ]
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Nascent chain (1 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- 1,4-diaminobutane (88 Da, Ligand)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
- Escherichia coli paused disome complex (2 MDa, Complex from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Trna-val (a/p-site) (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul1 (24 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
- Trna-trp (p/e-site) (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- Messenger rna (19 kDa, RNA from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- Trna-ala (a/p-site) (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s1 (61 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- Trna-phe (p/e-site) (24 kDa, RNA from Escherichia coli)
Structure of the 30S-IF3 complex from Escherichia coli
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8jsg
Q-score: 0.265
Proteins (2023) [ DOI: doi:10.1002/prot.26655 Pubmed: 38148682 ]
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs21 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us7 (16 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (25 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us5 (16 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us13 (12 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us3 (23 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs6, non-modified isoform (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Translation initiation factor if-3 (20 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- Complex of the small ribosomal subunit (30s) and translation initiation factor 3 (if3) in escherichia coli (850 kDa, Complex from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Initiation factor 3 (Cellular component from Escherichia coli)
- 30s subunit of ribosome (Cellular component)
E. coli plasmid-borne JetABCD(E248A) core in a cleavage-competent state
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 8q72
Q-score: 0.307
Roisne-Hamelin F, Liu HW, Taschner M, Li Y, Gruber S
Mol Cell (2024) 84 pp. 883- [ Pubmed: 38309275 DOI: doi:10.1016/j.molcel.2024.01.009 ]
- Jetc (124 kDa, Protein from Escherichia coli)
- Jetabcd(e248a) loaded onto plasmid dna (Complex from Escherichia coli)
- Jetd(e248a) (43 kDa, Protein from Escherichia coli)
- Jetb (28 kDa, Protein from Escherichia coli)
- Circular plasmid dna (1840-mer) (12 kDa, DNA from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Jeta (57 kDa, Protein from Escherichia coli)
Structure of the 30S-body-IF3 complex from Escherichia coli
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8jsh
Q-score: 0.294
Proteins (2023) [ DOI: doi:10.1002/prot.26655 Pubmed: 38148682 ]
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- Translation initiation factor if-3 (20 kDa, Protein from Escherichia coli)
- Body of the 30s subunit of ribosome (Cellular component)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- Complex of the small ribosomal subunit (30s) body and translation initiation factor 3 (if3) in escherichia coli (Complex from Escherichia coli)
- 16s ribosomal rna (498 kDa, RNA from Escherichia coli)
- Initiation factor 3 (Cellular component from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
Structure of bacterial ribosome determined by cryoEM at 100 keV
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8pva
Q-score: 0.287
McMullan G, Naydenova K, Mihaylov D, Yamashita K, Peet MJ, Wilson H, Dickerson JL, Chen S, Cannone G, Lee Y, Hutchings KA, Gittins O, Sobhy MA, Wells T, El-Gomati MM, Dalby J, Meffert M, Schulze-Briese C, Henderson R, Russo CJ
PNAS (2023) 120 pp. e2312905120-e2312905120 [ DOI: doi:10.1073/pnas.2312905120 Pubmed: 38011573 ]
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- P-site trna-fmet (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- A-site trna-val (24 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
- 23s rrna (941 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)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- E-site trna (589 Da, RNA from Escherichia coli)
- Small ribosomal subunit protein bs6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- Mrna (9 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
Structure of TolQR complex from E.coli
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8odt
Q-score: 0.198
Williams-Jones DP, Webby MN, Press CE, Gradon JM, Armstrong SR, Szczepaniak J, Kleanthous C
PNAS (2023) 120 pp. e2306707120-e2306707120 [ DOI: doi:10.1073/pnas.2306707120 Pubmed: 37972066 ]
- Tol-pal system protein tolq (25 kDa, Protein from Escherichia coli K-12)
- Tolq-tolr 5:2 complex (170 kDa, Complex from Escherichia coli)
- Tol-pal system protein tolr (20 kDa, Protein from Escherichia coli K-12)
CX3CR1 nucleosome bound PU.1 and C/EBPa
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8evj
Q-score: 0.31
Lian T, Guan R, Zhou BR, Bai Y
Nat Struct Mol Biol (2024) 31 pp. 633-643 [ Pubmed: 38267599 DOI: doi:10.1038/s41594-023-01189-z ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Scfv (29 kDa, Protein from Escherichia coli)
- Transcription factor pu.1 (32 kDa, Protein from Mus musculus)
- Dna (167-mer) (51 kDa, DNA from Mus musculus)
- Nucleosome complexed with pu.1 and c/ebpa (Complex from Mus musculus)
- Dna (167-mer) (51 kDa, DNA from Mus musculus)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)