human delta-METTL18 60S ribosome
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7f5s
Q-score: 0.561
Matsuura-Suzuki E, Shimazu T, Takahashi M, Kotoshiba K, Suzuki T, Kashiwagi K, Sohtome Y, Akakabe M, Sodeoka M, Dohmae N, Ito T, Shinkai Y, Iwasaki S
eLife (2022) 11 [ DOI: doi:10.7554/eLife.72780 Pubmed: 35674491 ]
- 60s ribosomal protein l39 (6 kDa, Protein from Human)
- 5.8s rrna (50 kDa, RNA from Human)
- 60s ribosomal protein l41 (3 kDa, Protein from Human)
- 60s ribosomal protein l23 (14 kDa, Protein from Human)
- 60s ribosomal protein l9 (21 kDa, Protein from Human)
- 60s ribosomal protein l30 (12 kDa, Protein from Human)
- 60s ribosomal protein l8 (28 kDa, Protein from Human)
- 60s ribosomal protein l35 (14 kDa, Protein from Human)
- 60s ribosomal protein l24 (17 kDa, Protein from Human)
- 60s ribosomal protein l3 (46 kDa, Protein from Human)
- 60s ribosomal protein l29 (17 kDa, Protein from Human)
- 60s ribosomal protein l31 (14 kDa, Protein from Human)
- 60s ribosomal protein l6 (32 kDa, Protein from Human)
- 60s ribosomal protein l36a (12 kDa, Protein from Human)
- 60s (Complex from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Human)
- 60s ribosomal protein l36 (12 kDa, Protein from Human)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l11 (20 kDa, Protein from Human)
- 60s ribosomal protein l13a (23 kDa, Protein from Human)
- 60s ribosomal protein l5 (34 kDa, Protein from Human)
- 60s ribosomal protein l15 (24 kDa, Protein from Human)
- 60s ribosomal protein l23a (17 kDa, Protein from Human)
- 60s ribosomal protein l27 (15 kDa, Protein from Human)
- 60s ribosomal protein l4 (47 kDa, Protein from Human)
- 28s rrna (1 MDa, RNA from Human)
- 60s ribosomal protein l7a (30 kDa, Protein from Human)
- Water (18 Da, Ligand)
- 60s ribosomal protein l10 (24 kDa, Protein from Human)
- 60s ribosomal protein l26 (17 kDa, Protein from Human)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Human)
- 60s ribosomal protein l18 (21 kDa, Protein from Human)
- 60s ribosomal protein l32 (15 kDa, Protein from Human)
- 60s ribosomal protein l37a (10 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- 5s rrna (38 kDa, RNA from Human)
- 60s ribosomal protein l18a (20 kDa, Protein from Human)
- 60s ribosomal protein l21 (18 kDa, Protein from Human)
- 60s ribosomal protein l14 (23 kDa, Protein from Human)
- 60s ribosomal protein l22 (14 kDa, Protein from Human)
- 60s ribosomal protein l17 (21 kDa, Protein from Human)
- 60s ribosomal protein l7 (29 kDa, Protein from Human)
- 60s ribosomal protein l13 (24 kDa, Protein from Human)
- 60s ribosomal protein l35a (12 kDa, Protein from Human)
- 60s ribosomal protein l28 (15 kDa, Protein from Human)
- 60s ribosomal protein l19 (23 kDa, Protein from Human)
- 60s ribosomal protein l27a (16 kDa, Protein from Human)
- 60s ribosomal protein l37 (11 kDa, Protein from Human)
- 60s ribosomal protein l38 (8 kDa, Protein from Human)
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in inactivated conformation (Dataset-A)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7tdg
Q-score: 0.386
eLife (2022) 11 [ Pubmed: 35257661 DOI: doi:10.7554/eLife.75568 ]
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Rabbit ryr1 with amp-pcp and high ca2+ in nanodisc (2 MDa, Complex from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor 1,ryr1 (533 kDa, Protein from rabbit)
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in open conformation
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7tdh
Q-score: 0.215
eLife (2022) 11 [ Pubmed: 35257661 DOI: doi:10.7554/eLife.75568 ]
- Rabbit ryr1 with amp-pcp and high ca2+ in nanodisc (2 MDa, Complex from Oryctolagus cuniculus)
- Ryanodine receptor 1,ryanodine receptor 1,ryr1 (533 kDa, Protein from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7tdi
Q-score: 0.332
eLife (2022) 11 [ Pubmed: 35257661 DOI: doi:10.7554/eLife.75568 ]
- Rabbit ryr1 with amp-pcp and high ca2+ in nanodisc (2 MDa, Complex from Oryctolagus cuniculus)
- Ryanodine receptor 1,ryanodine receptor 1,ryr1 (533 kDa, Protein from rabbit)
- Calcium ion (40 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7tdj
Q-score: 0.365
eLife (2022) 11 [ Pubmed: 35257661 DOI: doi:10.7554/eLife.75568 ]
- Rabbit ryr1 with amp-pcp and high ca2+ in nanodisc (2 MDa, Complex from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- Ryanodine receptor 1,ryanodine receptor 1,ryr1 (533 kDa, Protein from rabbit)
- Calcium ion (40 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7tdk
Q-score: 0.357
eLife (2022) 11 [ Pubmed: 35257661 DOI: doi:10.7554/eLife.75568 ]
- Rabbit ryr1 with amp-pcp and high ca2+ in nanodisc (2 MDa, Complex from Oryctolagus cuniculus)
- Ryanodine receptor 1,ryanodine receptor 1,ryr1 (533 kDa, Protein from rabbit)
- Calcium ion (40 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7pd3
Q-score: 0.394
Chandrasekaran V, Desai N, Burton NO, Yang H, Price J, Miska EA, Ramakrishnan V
eLife (2021) 10 [ DOI: doi:10.7554/eLife.68806 Pubmed: 34609277 ]
- Human mitoribosomal large subunit assembly intermediate (Complex from Homo sapiens)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Human)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Human)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Human)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Human)
- Pseudouridine-5'-monophosphate (324 Da, Ligand)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Human)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Human)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Human)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Human)
- 5-methylcytosine rrna methyltransferase nsun4 (43 kDa, Protein from Human)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Human)
- Acyl carrier protein, mitochondrial (17 kDa, Protein from Human)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Human)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Human)
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Human)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Human)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Human)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Human)
- S-adenosylmethionine (398 Da, Ligand)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Human)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Human)
- Mief1 upstream open reading frame protein (8 kDa, Protein from Human)
- 39s ribosomal protein l45, mitochondrial (35 kDa, Protein from Human)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Human)
- Cytidine-5'-monophosphate (323 Da, Ligand)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Human)
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-monophosphate (363 Da, Ligand)
- O2'-methylguanosine-5'-monophosphate (377 Da, Ligand)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Human)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Human)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Human)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Human)
- Ml65 (2 kDa, Protein from Human)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Human)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Human)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Human)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Human)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Human)
- 16s rrna (500 kDa, RNA from Human)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Human)
- Mitochondrial assembly of ribosomal large subunit protein 1 (26 kDa, Protein from Human)
- Mitochondrial ribosome-associated gtpase 1 (37 kDa, Protein from Human)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Human)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Human)
- 39s ribosomal protein l18, mitochondrial (20 kDa, Protein from Human)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Human)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Human)
- 39s ribosomal protein l22, mitochondrial (23 kDa, Protein from Human)
- Mt-trnaval (22 kDa, RNA from Human)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Human)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Human)
- Uridine-5'-monophosphate (324 Da, Ligand)
- 39s ribosomal protein l50, mitochondrial (18 kDa, Protein from Human)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Human)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Human)
- 4'-phosphopantetheine (358 Da, Ligand)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Human)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Human)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Human)
- Transcription termination factor 4, mitochondrial (44 kDa, Protein from Human)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Human)
- Adenosine-5'-monophosphate (347 Da, Ligand)
Legionella pneumophila Dot/Icm T4SS OMC
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7mud
Q-score: 0.564
Sheedlo MJ, Durie CL, Chung JM, Chang L, Roberts J, Swanson M, Lacy DB, Ohi MD
eLife (2021) 10 [ Pubmed: 34519271 DOI: doi:10.7554/eLife.70427 ]
- Unknown protein fragment (783 Da, Protein from Legionella pneumophila)
- Dotc (34 kDa, Protein from Legionella pneumophila)
- Legionella pneumophila dot/icm t4ss omc (Complex from Legionella pneumophila)
- Duf2807 domain-containing protein (36 kDa, Protein from Legionella pneumophila)
- Type iv secretion protein icmk (38 kDa, Protein from Legionella pneumophila)
- Dotf (29 kDa, Protein from Legionella pneumophila)
- Neurogenic locus notch (13 kDa, Protein from Legionella pneumophila)
- Inner membrane lipoprotein yiad (21 kDa, Protein from Legionella pneumophila)
- Outer membrane protein, ompa family protein (27 kDa, Protein from Legionella pneumophila)
- Dotd (17 kDa, Protein from Legionella pneumophila)
Legionella pneumophila Dot/Icm T4SS PR
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7mue
Q-score: 0.601
Sheedlo MJ, Durie CL, Chung JM, Chang L, Roberts J, Swanson M, Lacy DB, Ohi MD
eLife (2021) 10 [ Pubmed: 34519271 DOI: doi:10.7554/eLife.70427 ]
- Legionella pneumophila dot/icm t4ss pr (Complex from Legionella pneumophila)
- Type iv secretion protein icmk (38 kDa, Protein from Legionella pneumophila)
- Dotf (29 kDa, Protein from Legionella pneumophila)
- Icme protein (107 kDa, Protein from Legionella pneumophila)
- Unknown protein fragment (4 kDa, Protein from Legionella pneumophila)
Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in nanodisc
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7k0t
Q-score: 0.332
eLife (2022) 11 [ Pubmed: 35257661 DOI: doi:10.7554/eLife.75568 ]
- Zinc ion (65 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Ryr1 (533 kDa, Protein from Oryctolagus cuniculus)
- Rabbit ryr1 with amp-pcp (2 MDa, Complex from Oryctolagus cuniculus)