Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 8qoi
Q-score: 0.669
Holvec S, Barchet C, Lechner A, Frechin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Nat Struct Mol Biol (2024) 31 pp. 1251-1264 [ DOI: doi:10.1038/s41594-024-01274-x Pubmed: 38844527 ]
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 5s rrna (120-mer) (38 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el6 (28 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- Ubiquitin-like fubi-ribosomal protein es30 fusion protein (14 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 18s rrna (1740-mer) (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul30 (29 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul18 (34 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul15 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10-like (24 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul3 (46 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 28s rrna (3773-mer) (1 MDa, RNA from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul4 (41 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- 5.8s rrna (156-mer) (50 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- Human 80s ribosome (4 MDa, Complex from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
Holvec S, Barchet C, Lechner A, Frechin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Nat Struct Mol Biol (2024) 31 pp. 1251-1264 [ DOI: doi:10.1038/s41594-024-01274-x Pubmed: 38844527 ]
Holvec S, Barchet C, Lechner A, Frechin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Nat Struct Mol Biol (2024) 31 pp. 1251-1264 [ DOI: doi:10.1038/s41594-024-01274-x Pubmed: 38844527 ]
Holvec S, Barchet C, Lechner A, Frechin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Nat Struct Mol Biol (2024) 31 pp. 1251-1264 [ DOI: doi:10.1038/s41594-024-01274-x Pubmed: 38844527 ]
Holvec S, Barchet C, Lechner A, Frechin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Nat Struct Mol Biol (2024) 31 pp. 1251-1264 [ DOI: doi:10.1038/s41594-024-01274-x Pubmed: 38844527 ]
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7qhm
Q-score: 0.567
Kao WC, 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. 545-545 [ Pubmed: 35087070 DOI: doi:10.1038/s41467-022-28179-x ]
- Oxygen molecule (31 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)
- Heme c (618 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Azide ion (42 Da, Ligand)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Copper (ii) ion (63 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Water (18 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Heme-as (920 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Palmitic acid (256 Da, Ligand)
- Stigmatellin a (514 Da, Ligand)
- Protoporphyrin ix containing fe (616 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)
- Diacyl glycerol (625 Da, Ligand)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- [(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)
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- [ Pubmed: 35087070 DOI: doi:10.1038/s41467-022-28179-x ]
- [(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)
- Heme c (618 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Copper (ii) ion (63 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Water (18 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Heme-as (920 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Diacyl glycerol (625 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)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- [(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)
Volta phase plate data collection facilitates image processing and cryo-EM structure determination
von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Menetret JF, Klaholz BP
J Struct Biol (2018) [ Pubmed: 29337113 DOI: doi:10.1016/j.jsb.2018.01.003 ]
- Ribosome (Complex from Homo sapiens)
Volta phase plate data collection facilitates image processing and cryo-EM structure determination
von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Menetret JF, Klaholz BP
J Struct Biol (2018) [ Pubmed: 29337113 DOI: doi:10.1016/j.jsb.2018.01.003 ]
- Ribosome (Complex from Homo sapiens)
Volta phase plate data collection facilitates image processing and cryo-EM structure determination
von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Menetret JF, Klaholz BP
J Struct Biol (2018) 202 pp. 191-199 [ Pubmed: 29337113 DOI: doi:10.1016/j.jsb.2018.01.003 ]
- Ribosome (Complex from Homo sapiens)