Structure of Mycobacterium smegmatis HflX bound to a 70S ribosome
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8vio
Q-score: 0.486
Majumdar S, Kashyap A, Koripella RK, Sharma MR, Hurst-Hess K, Manjari SR, Banavali NK, Ghosh P, Agrawal RK
PNAS (2025) 122 pp. e2419826122-e2419826122 [ Pubmed: 39913204 DOI: doi:10.1073/pnas.2419826122 ]
- 50s ribosomal protein l33 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l10 (18 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l11 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s13 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l31 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l23 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l17 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s15 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s ribosomal rna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s8 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s7 (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s6 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Conserved domain protein (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s16 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s ribosomal rna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s17 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s12 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l21 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l30 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l22 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s14 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 16s ribosomal rna (495 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- E-trna (24 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l3 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s10 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s20 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s4 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s11 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis 70s ribosome bound to hflx-gmppcp complex (Complex from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s9 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Gtpase hflx (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s18 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s19 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s3 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of Light-harvesting complex from Spinacia oleracea
Resolution: 2.17 Å
EM Method: Single-particle
Fitted PDBs: 8y15
Q-score: 0.709
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ Pubmed: 39346626 DOI: doi:10.1093/pnasnexus/pgae405 ]
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- Light-harvesting complex ii from spinacia oleracea (700 kDa, Complex from Spinacia oleracea)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lutein (568 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
Cryo-EM structure of in vitro reconstituted Light-harvesting complex II trimer
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8yee
Q-score: 0.678
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ Pubmed: 39346626 DOI: doi:10.1093/pnasnexus/pgae405 ]
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Spinacia oleracea)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- In vitro reconstituted light-harvesting complex ii (120 kDa, Complex from Spinacia oleracea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lutein (568 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
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 [ Pubmed: 39531492 DOI: doi:10.1073/pnas.2412780121 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Lansoprazole sulfide (353 Da, Ligand)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, 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)
- Heme c (618 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)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Water (18 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Heme-a (852 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Tridecane (184 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Cardiolipin (1 kDa, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 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 [ Pubmed: 39531492 DOI: doi:10.1073/pnas.2412780121 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, 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)
- Heme c (618 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)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Water (18 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Heme-a (852 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Tridecane (184 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Cardiolipin (1 kDa, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
Nematostella vectensis TRPM2 tetramer in complex with ADPRP/Ca2+
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 9jje
Q-score: 0.488
Toth B, Jiang Y, Szollosi A, Zhang Z, Csanady L
PNAS (2024) 121 pp. e2415548121-e2415548121 [ Pubmed: 39514307 DOI: doi:10.1073/pnas.2415548121 ]
- Transient receptor potential cation channel subfamily m member-like 2 (176 kDa, Protein from Nematostella vectensis)
- Nvtrpm2 tetramer in complex with adprp/ca2+ (700 kDa, Complex from Nematostella vectensis)
- Calcium ion (40 Da, Ligand)
- [(2r,3r,4r,5r)-5-(6-amino-9h-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2r,3s,4r,5r)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (639 Da, Ligand)
Nematostella vectensis TRPM2 protomer in complex with ADPRP/Ca2+
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 9jjf
Q-score: 0.544
Toth B, Jiang Y, Szollosi A, Zhang Z, Csanady L
PNAS (2024) 121 pp. e2415548121-e2415548121 [ Pubmed: 39514307 DOI: doi:10.1073/pnas.2415548121 ]
- Transient receptor potential cation channel subfamily m member-like 2 (176 kDa, Protein from Nematostella vectensis)
- Calcium ion (40 Da, Ligand)
- Nvtrpm2 protomer in complex with adprp/ca2+ (170 kDa, Complex from Nematostella vectensis)
- [(2r,3r,4r,5r)-5-(6-amino-9h-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2r,3s,4r,5r)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (639 Da, Ligand)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9c0q
Q-score: 0.56
Biester A, Grahame DA, Drennan CL
PNAS (2024) 121 pp. e2410995121-e2410995121 [ Pubmed: 39361653 DOI: doi:10.1073/pnas.2410995121 ]
- Acetyl-coa decarbonylase/synthase complex (212 kDa, Complex from Methanosarcina thermophila)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit alpha 2 (87 kDa, Protein from Methanosarcina thermophila)
- Iron/sulfur cluster (351 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit epsilon 2 (18 kDa, Protein from Methanosarcina thermophila)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9c0r
Q-score: 0.625
Biester A, Grahame DA, Drennan CL
PNAS (2024) 121 pp. e2410995121-e2410995121 [ Pubmed: 39361653 DOI: doi:10.1073/pnas.2410995121 ]
- Acetyl-coa decarbonylase/synthase complex (212 kDa, Complex from Methanosarcina thermophila)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit alpha 2 (87 kDa, Protein from Methanosarcina thermophila)
- Iron/sulfur cluster (351 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit epsilon 2 (18 kDa, Protein from Methanosarcina thermophila)
- Water (18 Da, Ligand)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9c0s
Q-score: 0.569
Biester A, Grahame DA, Drennan CL
PNAS (2024) 121 pp. e2410995121-e2410995121 [ Pubmed: 39361653 DOI: doi:10.1073/pnas.2410995121 ]
- Fe3-s4 cluster (295 Da, Ligand)
- Nickel (ii) ion (58 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit beta 2 (52 kDa, Protein from Methanosarcina thermophila)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex (265 kDa, Complex from Methanosarcina thermophila)
- Acetyl-coa decarbonylase/synthase complex subunit alpha 2 (87 kDa, Protein from Methanosarcina thermophila)
- Carbon monoxide (28 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit epsilon 2 (18 kDa, Protein from Methanosarcina thermophila)