Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7qho
Q-score: 0.516
Kao W-C, Ortmann de Percin Northumberland C, Cheng TC, Ortiz J, Durand A, von Loeffelholz O, Schilling O, Biniossek ML, Klaholz BP, Hunte C
Nat Commun (2022) 13 pp. 545- [ DOI: doi:10.1038/s41467-022-28179-x Pubmed: 35087070 ]
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{r},4~{s},5~{s},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{s})-10-methylhenicosanoate (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Calcium ion (40 Da, Ligand)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dinuclear copper ion (127 Da, Ligand)
- Heme c (618 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Water (18 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Diacyl glycerol (625 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme-as (920 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{s},4~{s},5~{r},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{r})-10-methyldodecanoate (1 kDa, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Capsid of empty GTA particle computed with C5 symmetry
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 6tsu
Q-score: 0.532
Bardy P, Fuzik T, Hrebik D, Pantucek R, Thomas Beatty J, Plevka P
Nat Commun (2020) 11 pp. 3034-3034 [ DOI: doi:10.1038/s41467-020-16669-9 Pubmed: 32541663 ]
- Rhodobacter capsulatus de442 gene transfer agent capsid (80 kDa, Complex from Rhodobacter capsulatus DE442)
- Uncharacterized protein (32 kDa, Protein from Rhodobacter capsulatus DE442)
- Head spike (Complex from Rhodobacter capsulatus DE442)
- Major capsid protein rcc01687 (40 kDa, Protein from Rhodobacter capsulatus DE442)
- Uncharacterized protein (9 kDa, Protein from Rhodobacter capsulatus DE442)
The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 6ywv
Q-score: 0.544
Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A
Nat Commun (2020) 11 pp. 5187-5187 [ Pubmed: 33056988 DOI: doi:10.1038/s41467-020-18830-w ]
- Mitochondrial ribosomal protein l43 (15 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein subunit l32 (14 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (49 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein subunit l23 (26 kDa, Protein from Neurospora crassa OR74A)
- Assembly intermediate of the mitoribosome of neurospora crassa (Complex from Neurospora crassa OR74A)
- 60s ribosomal protein l6 (28 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (14 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (11 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l17 (22 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (23 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l20 (25 kDa, Protein from Neurospora crassa OR74A)
- Rnase iii domain-containing protein (29 kDa, Protein from Neurospora crassa OR74A)
- 54s ribosomal protein l4, mitochondrial (29 kDa, Protein from Neurospora crassa OR74A)
- 23 s rrna (1 MDa, RNA from Neurospora crassa OR74A)
- Ribosomal protein (13 kDa, Protein from Neurospora crassa OR74A)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 50s ribosomal subunit protein l15 (33 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l30 (18 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (37 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial large ribosomal subunit yml35 (50 kDa, Protein from Neurospora crassa OR74A)
- Spermine (202 Da, Ligand)
- Uncharacterized protein (18 kDa, Protein from Neurospora crassa OR74A)
- Kow domain-containing protein (45 kDa, Protein from Neurospora crassa OR74A)
- Potassium ion (39 Da, Ligand)
- Uncharacterized protein (7 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l24 (31 kDa, Protein from Neurospora crassa OR74A)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l16 (27 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l3 (41 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein (28 kDa, Protein from Neurospora crassa OR74A)
- Atpase synthesis protein 25, mitochondrial (77 kDa, Protein from Neurospora crassa OR74A)
- Aconitate hydratase (23 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (41 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial large ribosomal subunit (41 kDa, Protein from Neurospora crassa OR74A)
- 54s ribosomal protein l31, mitochondrial (13 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (23 kDa, Protein from Neurospora crassa OR74A)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l5 (39 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l2 (42 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal subunit l30 (41 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l14 (14 kDa, Protein from Neurospora crassa OR74A)
- Ribosomal protein l13 (20 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l4, variant (36 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l19 (16 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein l44 (11 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (32 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (49 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l3 (48 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial 60s ribosomal protein l25 (18 kDa, Protein from Neurospora crassa OR74A)
CryoEM structure of the narrow type IV pilus (PilA5) from Thermus thermophilus
Resolution: 3.49 Å
EM Method: Helical reconstruction
Fitted PDBs: 6xxe
Q-score: 0.252
Neuhaus A, Selvaraj M, Salzer R, Langer JD, Kruse K, Kirchner L, Sanders K, Daum B, Averhoff B, Gold VAM
Nat Commun (2020) 11 pp. 2231-2231 [ Pubmed: 32376942 DOI: doi:10.1038/s41467-020-15650-w ]
Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 6szs
Q-score: 0.535
Shimokawa-Chiba N, Muller C, Fujiwara K, Beckert B, Ito K, Wilson DN, Chiba S
Nat Commun (2019) 10 pp. 5397-5397 [ DOI: doi:10.1038/s41467-019-13408-7 Pubmed: 31776341 ]
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli ribosome with p-site trna-pro(cgg, carrying the nascent chain (Complex from Escherichia coli K-12)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- Mrna (1 kDa, RNA from Escherichia coli K-12)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- Uncharacterized protein yqkk (8 kDa, Protein from Bacillus subtilis (strain 168))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli (strain K12))
- Bacillus subtilis ribosome rescue factor (brfa; former yqkk) and peptide chain release factor 2 (rf2) (Complex from Bacillus subtilis (strain 168))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
- P-site trna-pro(cgg) (24 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- E. coli 70s stalled on truncated mrna in complex bsbrfa and bsrf2-q251p (Complex)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli (strain K12))
- Peptide chain release factor 2 (41 kDa, Protein from Bacillus subtilis (strain 168))
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 6h82
Q-score: 0.389
Santos-Perez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA
Nat Commun (2019) 10 pp. 1184-1184 [ DOI: doi:10.1038/s41467-019-08927-2 Pubmed: 30862777 ]
- Uncharacterized protein (14 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Vp16 (vertex complex) (18 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Haloarcula hispanica icosahedral virus 2 (Virus from Haloarcula hispanica icosahedral virus 2)
- Vp4 (25 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Vp7 (17 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Vp7 (18 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Vp7 (18 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Gps iii (8 kDa, Protein from Haloarcula hispanica icosahedral virus 2)
- Polypeptide stretch (vertex complex) (2 kDa, Protein from Haloarcula hispanica icosahedral virus 2)