Cryo-EM structure of human SOD1 (WT) amyloid filament
Resolution: 3.39 Å
EM Method: Helical reconstruction
Fitted PDBs: 9jbo
Q-score: 0.475
Baek Y, Kim H, Lee D, Kim D, Jo E, Roh SH, Ha NC
PNAS (2025) 122 pp. e2408582122-e2408582122 [ Pubmed: 39874287 DOI: doi:10.1073/pnas.2408582122 ]
- Superoxide dismutase [cu-zn] (16 kDa, Protein from Homo sapiens)
- Amyloid filament of human wild-type sod1 protein (34 MDa, Complex from Homo sapiens)
Cryo-EM structure of human SOD1 (C6A/C111A) amyloid filament
Resolution: 3.18 Å
EM Method: Helical reconstruction
Fitted PDBs: 9jbp
Q-score: 0.488
Baek Y, Kim H, Lee D, Kim D, Jo E, Roh SH, Ha NC
PNAS (2025) 122 pp. e2408582122-e2408582122 [ Pubmed: 39874287 DOI: doi:10.1073/pnas.2408582122 ]
- Unassigned poly-alanine model (698 Da, Protein from Homo sapiens)
- Amyloid filament of human c6a/c111a mutant sod1 protein (69 MDa, Complex from Homo sapiens)
- Superoxide dismutase [cu-zn] (16 kDa, Protein from Homo sapiens)
CIII2/CIV respiratory supercomplex from Mycobacterium smegmatis with lansoprazole sulfide
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9ftz
Q-score: 0.608
Kovalova T, Krol S, Gamiz-Hernandez AP, Sjostrand D, Kaila VRI, Brzezinski P, Hogbom M
PNAS (2024) 121 pp. e2412780121-e2412780121 [ DOI: doi:10.1073/pnas.2412780121 Pubmed: 39531492 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- [(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)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Tridecane (184 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Lansoprazole sulfide (353 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Palmitic acid (256 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
CIII2/CIV respiratory chain supercomplex from Mycobacterium smegmatis
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9fu0
Q-score: 0.573
Kovalova T, Krol S, Gamiz-Hernandez AP, Sjostrand D, Kaila VRI, Brzezinski P, Hogbom M
PNAS (2024) 121 pp. e2412780121-e2412780121 [ DOI: doi:10.1073/pnas.2412780121 Pubmed: 39531492 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- [(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)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Tridecane (184 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Palmitic acid (256 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of an amyloid fibril formed by ALS-causing SOD1 mutation G85R
Resolution: 2.97 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ihu
Q-score: 0.568
Wang LQ, Ma YY, Zhang MY, Yuan HY, Li XN, Zhao K, Chen J, Li D, Wang ZZ, Le WD, Liu C, Liang Y
Sci Adv (2024) [ ]
- Als-causing sod1 mutations g85r (Cellular component from Homo sapiens)
- Superoxide dismutase [cu-zn] (16 kDa, Protein from Homo sapiens)
Cryo-EM structure of an amyloid fibril formed by ALS-causing SOD1 mutation H46R
Resolution: 3.11 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ihv
Q-score: 0.549
Wang LQ, Ma YY, Zhang MY, Yuan HY, Li XN, Zhao K, Chen J, Li D, Wang ZZ, Le WD, Liu C, Liang Y
Sci Adv (2024) [ ]
- Als-causing sod1 mutations h46r (Cellular component from Homo sapiens)
- Superoxide dismutase [cu-zn] (15 kDa, Protein from Homo sapiens)
Mycobacterial supercomplex malate:quinone oxidoreductase assembly
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dm1
Q-score: 0.38
Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung J, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein J
To Be Published
- Respiratory complex mqo:ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Heme c (618 Da, Ligand)
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Probable malate:quinone oxidoreductase (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Palmitic acid (256 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cardiolipin (1 kDa, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ovc
Q-score: 0.598
Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI
Nat Commun (2024) 15 pp. 5276-5276 [ DOI: doi:10.1038/s41467-024-49628-9 Pubmed: 38902248 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (869 Da, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Palmitic acid (256 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Co-purified unknown peptide (2 kDa, Protein from Mycolicibacterium smegmatis)
Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8ovd
Q-score: 0.699
Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI
Nat Commun (2024) 15 pp. 5276-5276 [ DOI: doi:10.1038/s41467-024-49628-9 Pubmed: 38902248 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- [(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)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Tridecane (184 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Palmitic acid (256 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of amyloid fibril formed by full-length human SOD1
Resolution: 2.95 Å
EM Method: Helical reconstruction
Fitted PDBs: 7vzf
Q-score: 0.244
Wang LQ, Ma Y, Yuan HY, Zhao K, Zhang MY, Wang Q, Huang X, Xu WC, Dai B, Chen J, Li D, Zhang D, Wang Z, Zou L, Yin P, Liu C, Liang Y
Nat Commun (2022) 13 pp. 3491-3491 [ DOI: doi:10.1038/s41467-022-31240-4 Pubmed: 35715417 ]
- Superoxide dismutase [cu-zn] (15 kDa, Protein from Homo sapiens)
- Human sod1 amyloid fibril (Cellular component from Homo sapiens)