Structure of a BAM/EspP(beta9-12) hybrid-barrel intermediate
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ri4
Q-score: 0.442
Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N
Nat Commun (2021) 12 pp. 7131-7131 [ Pubmed: 34880256 DOI: doi:10.1038/s41467-021-27449-4 ]
- Outer membrane protein assembly factor bamc (36 kDa, Protein from Escherichia coli)
- Esppbeta9-12 (8 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamb (39 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamd (27 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bame (13 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bama (90 kDa, Protein from Escherichia coli)
- Structure of a bam/espp hybrid-barrel intermediate (290 MDa, Complex from Escherichia coli)
Structure of a BAM in MSP1E3D1 nanodiscs at 4 Angstrom resolution
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7ri5
Q-score: 0.385
Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N
Nat Commun (2021) 12 pp. 7131-7131 [ Pubmed: 34880256 DOI: doi:10.1038/s41467-021-27449-4 ]
- Outer membrane protein assembly factor bamc (36 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamd (27 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bame (13 kDa, Protein from Escherichia coli)
- Structure of bam in nanodisc using msp1e3d1 (210 MDa, Complex from Escherichia coli)
- Outer membrane protein assembly factor bamb (41 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bama (90 kDa, Protein from Escherichia coli)
Structure of BAM in MSP1E3D1 nanodiscs prepared from E. coli outer membranes
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 7ri6
Q-score: 0.2
Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N
Nat Commun (2021) 12 pp. 7131-7131 [ Pubmed: 34880256 DOI: doi:10.1038/s41467-021-27449-4 ]
- Outer membrane protein assembly factor bamc (36 kDa, Protein from Escherichia coli)
- Structure of bam in msp nanodiscs prepared from native membranes (210 MDa, Complex from Escherichia coli)
- Outer membrane protein assembly factor bamd (27 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bame (13 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamb (41 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bama (90 kDa, Protein from Escherichia coli)
The structure of BAM in MSP1D1 nanodiscs
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7ri7
Q-score: 0.196
Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N
Nat Commun (2021) 12 pp. 7131-7131 [ Pubmed: 34880256 DOI: doi:10.1038/s41467-021-27449-4 ]
- Outer membrane protein assembly factor bamc (36 kDa, Protein from Escherichia coli)
- Structure of bam in nanodiscs using msp1d1 (210 MDa, Complex from Escherichia coli)
- Outer membrane protein assembly factor bamd (27 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bame (13 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamb (41 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bama (90 kDa, Protein from Escherichia coli)
The structure of BAM in MSP1E3D1 at 6.9 Angstrom resolution
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 7ri9
Q-score: 0.178
Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N
Nat Commun (2021) 12 pp. 7131-7131 [ Pubmed: 34880256 DOI: doi:10.1038/s41467-021-27449-4 ]
- Outer membrane protein assembly factor bamc (36 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamd (27 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bame (13 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamb (41 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bama (90 kDa, Protein from Escherichia coli)
- Structure of bam in nanodiscs using msp1e3d1 (210 MDa, Complex from Escherichia coli)
The structure of BAM in complex with EspP at 7 Angstrom resolution
Resolution: 7.0 Å
EM Method: Single-particle
Fitted PDBs: 7rj5
Q-score: 0.21
Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N
Nat Commun (2021) 12 pp. 7131-7131 [ Pubmed: 34880256 DOI: doi:10.1038/s41467-021-27449-4 ]
- Maltodextrin-binding protein,autotransporter outer membrane beta-barrel domain-containing protein chimera (79 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bama (90 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamb (39 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Outer membrane protein assembly factor bamc (36 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bame (13 kDa, Protein from Escherichia coli)
- Outer membrane protein assembly factor bamd (27 kDa, Protein from Escherichia coli)
- Structure of a bam/espp hybrid-barrel intermediate (290 MDa, Complex from Escherichia coli)
Initiated 70S ribosome in complex with 2A protein from encephalomyocarditis virus (EMCV)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 7nwt
Q-score: 0.614
Hill CH, Pekarek L, Napthine S, Kibe A, Firth AE, Graham SC, Caliskan N, Brierley I
Nat Commun (2021) 12 pp. 7166- [ DOI: doi:10.1038/s41467-021-27400-7 ]
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- Protein 2a (17 kDa, Protein from Mengo encephalomyocarditis virus)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA 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)
- 50s ribosomal protein l11 (14 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 s6 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 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)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Mrna (37 kDa, RNA from Encephalomyocarditis virus)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 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)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein 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)
- Initiated 70s ribosome in complex with 2a protein from encephalomyocarditis virus (emcv) (Complex)
- 50s ribosomal protein l3 (22 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)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein 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)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- Fmet-nh-trna(fmet) (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- N-formylmethionine (177 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
ATP-bound AMP-activated protein kinase
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7m74
Q-score: 0.27
Yan Y, Mukherjee S, Harikumar KG, Strutzenberg TS, Zhou XE, Suino-Powell K, Xu TH, Sheldon RD, Lamp J, Brunzelle JS, Radziwon K, Ellis A, Novick SJ, Vega IE, Jones RG, Miller LJ, Xu HE, Griffin PR, Kossiakoff AA, Melcher K
Science (2021) 373 pp. 413-419 [ DOI: doi:10.1126/science.abe7565 Pubmed: 34437114 ]
- 5'-amp-activated protein kinase subunit beta-2 (22 kDa, Protein from Homo sapiens)
- Adenosine monophosphate (347 Da, Ligand)
- Fab light chain (22 kDa, Protein from Homo sapiens)
- Nanobody (13 kDa, Protein from Lama glama)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Fab heavy chain (24 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 5'-amp-activated protein kinase subunit gamma-1 (34 kDa, Protein from Homo sapiens)
- 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine (399 Da, Ligand)
- Mbp-fused atp bound ampk in complex with c-compound stabilized by fab and a nanobody (Complex from Homo sapiens)
- Maltose/maltodextrin abc transporter substrate-binding protein male (40 kDa, Protein from Escherichia coli)
- 5'-amp-activated protein kinase catalytic subunit alpha-1 (56 kDa, Protein from Homo sapiens)
Complete Bacterial 30S ribosomal subunit assembly complex state I (Consensus Refinement)
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 7nax
Q-score: 0.389
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR
Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abf7547 Pubmed: 34088665 ]
- 30s ribosomal protein s10 (11 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)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 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)
- Complete bacterial 30s ribosomal subunit assembly complex state i (consensus refinement) (Complex from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7cpj
Q-score: 0.502
Fujita T, Yokoyama T, Shirouzu M, Taguchi H, Ito T, Iwasaki S
RNA (2022) 28 pp. 290-302 [ Pubmed: 34906996 DOI: doi:10.1261/rna.078188.120 ]
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli KTE112)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli 2-427-07 S4 C3)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli KTE73)
- 16s ribosomal rna (498 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli MS 198-1)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli 2.3916)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli UMEA 3718-1)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli 2.3916)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli 907713)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli MS 117-3)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli 2-427-07 S4 C3)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli KTE112)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli 99.0741)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli 4.0522)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli O26:H11)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli O121:H19)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli 908573)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli KTE75)
- Isoleucine (131 Da, Ligand)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli KTE112)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli 99.0741)
- Proline (115 Da, Ligand)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli 113303)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli HVH 87 (4-5977630))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli 3-373-03 S4 C2)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli O177)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli KTE73)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli 2362-75)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli O7:K1 (strain IAI39 / ExPEC))
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli KTE64)
- P/p trna (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli G3/10)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli H461)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli M863)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli DEC1D)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli MS 84-1)
- Ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- Mrna (910 Da, RNA from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli TA054)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli H420)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)