Cryo-EM structure of the RC-dLH complex (model_1b) from Gemmatimonas phototrophica at 2.47 A
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 7o0w
Q-score: 0.624
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ DOI: doi:10.1126/sciadv.abk3139 Pubmed: 35171663 ]
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_1b (800 kDa, Complex from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Heme c (618 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 7o0x
Q-score: 0.629
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ DOI: doi:10.1126/sciadv.abk3139 Pubmed: 35171663 ]
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Heme c (618 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Rc-dlh model_2b (800 kDa, Complex from Gemmatimonas phototrophica)
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
III2-IV2 respiratory supercomplex from Corynebacterium glutamicum
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7q21
Q-score: 0.571
Moe A, Kovalova T, Krol S, Yanofsky DJ, Bott M, Sjostrand D, Rubinstein JL, Hogbom M, Brzezinski P
Structure (2022) 30 pp. 338- [ Pubmed: 34910901 DOI: doi:10.1016/j.str.2021.11.008 ]
- Cardiolipin (1 kDa, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Co-purified unknown peptide built as polyala (asce) (1 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Fe2/s2 (inorganic) cluster (175 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 bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Cytochrome c oxidase subunit 2 (39 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Magnesium ion (24 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Heme-as (920 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Uncharacterized protein cgl2664/cg2949 (20 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Co-purified unknown transmembrane helices built as polyala (ascd) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Co-purified unknown peptide built as polyala (asce) (1 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Tridecane (184 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- The respiratory supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Docosane (310 Da, Ligand)
Photosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 7bgi
Q-score: 0.629
Caspy I, Schwartz T, Bayro-Kaiser V, Fadeeva M, Kessel A, Ben-Tal N, Nelson N
Commun Biol (2021) 4 pp. 1380- [ DOI: doi:10.1038/s42003-021-02911-7 ]
- Photosystem i reaction center subunit iv, chloroplastic (7 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (20 kDa, Protein from Chlamydomonas reinhardtii)
- Lauric acid (200 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Chlamydomonas reinhardtii)
- (1~{s})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(4~{s})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol (568 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Photosystem i of temperature sensitive chlamydomonas reinhardtii (890 kDa, Complex from Chlamydomonas reinhardtii)
- Photosystem i reaction center subunit v, chloroplastic (9 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- Phosphatidylinositol (887 Da, Ligand)
- Photosystem i reaction center subunit psak, chloroplastic (8 kDa, Protein from Chlamydomonas reinhardtii)
- Phylloquinone (450 Da, Ligand)
- (3~{e},5~{e},7~{e})-6-methyl-8-[(6~{r})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one (260 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Octanoic acid (caprylic acid) (144 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit iii, chloroplastic (17 kDa, Protein from Chlamydomonas reinhardtii)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Psi subunit v (14 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chlamydomonas reinhardtii)
- Water (18 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ii, chloroplastic (16 kDa, Protein from Chlamydomonas reinhardtii)
- Sphingosine (299 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Chlamydomonas reinhardtii)
Structure of the translating Neurospora crassa ribosome arrested by cycloheximide
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7r81
Q-score: 0.539
Shen L, Su Z, Yang K, Wu C, Becker T, Bell-Pedersen D, Zhang J, Sachs MS
PNAS (2021) 118 [ Pubmed: 34815343 DOI: doi:10.1073/pnas.2111862118 ]
- 40s ribosomal protein s21 (9 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s6 (27 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l10 (25 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s29 (6 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s1 (29 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s20 (13 kDa, Protein from Neurospora crassa)
- Cytoplasmic ribosomal protein 10 (28 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s5 (23 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l20 (20 kDa, Protein from Neurospora crassa)
- Ribosomal_l28e domain-containing protein (16 kDa, Protein from Neurospora crassa)
- Ribosomal protein l19 (22 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l15 (24 kDa, Protein from Neurospora crassa)
- Trna (Complex from Neurospora crassa)
- 60s ribosomal protein l32 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s13 (16 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s4 (29 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s25 (10 kDa, Protein from Neurospora crassa)
- Ribosomal protein l37 (10 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s27 (8 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l6 (22 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l27 (el27) (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s8 (23 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s16 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s12 (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l23 (14 kDa, Protein from Neurospora crassa)
- Ribosomal protein l26 (15 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l8 (29 kDa, Protein from Neurospora crassa)
- 26s rrna (1 MDa, RNA from Neurospora crassa)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s11 (18 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l40 (6 kDa, Protein from Neurospora crassa)
- Nascent peptide (Complex from Neurospora crassa)
- 40s ribosomal protein s9 (21 kDa, Protein from Neurospora crassa)
- Nascent peptide (358 Da, Protein from Neurospora crassa)
- 60s ribosomal protein l22 (14 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s19 (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l36 (11 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l4-a (38 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l44 (11 kDa, Protein from Neurospora crassa)
- 40s ribosomal subunit (Complex from Neurospora crassa)
- Ribosomal protein s12 (17 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s7 (22 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s2 (28 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l3 (44 kDa, Protein from Neurospora crassa)
- Trna (24 kDa, RNA from Neurospora crassa)
- 40s ribosomal protein s18 (17 kDa, Protein from Neurospora crassa)
- 5.8s rrna (50 kDa, RNA from Neurospora crassa)
- 60s ribosomal protein l30 (11 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l17 (20 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s28 (7 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l38 (9 kDa, Protein from Neurospora crassa)
- Ribosomal protein srp1 (18 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l29 (7 kDa, Protein from Neurospora crassa)
- 4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
- 60s ribosomal protein l34 (13 kDa, Protein from Neurospora crassa)
- Hypothetical protein ncu16635 (el41) (3 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l7 (28 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s0 (31 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l39 (6 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l2 (27 kDa, Protein from Neurospora crassa)
- 18s rrna (578 kDa, RNA from Neurospora crassa)
- 60s ribosomal protein l9 (21 kDa, Protein from Neurospora crassa)
- Ubiquitin-40s ribosomal protein s27a (17 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l28 (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l35 (14 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l11 (20 kDa, Protein from Neurospora crassa)
- Mrna (Complex from Neurospora crassa)
- 60s ribosomal protein l18 (20 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l33 (12 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l24 (17 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s17 (16 kDa, Protein from Neurospora crassa)
- Ribosomal protein l14 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s26e (13 kDa, Protein from Neurospora crassa)
- 60s ribosomal subunit (Complex from Neurospora crassa)
- 60s ribosomal protein l16 (26 kDa, Protein from Neurospora crassa)
- Guanine nucleotide-binding protein subunit beta-like protein (35 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s14 (us11) (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l5 (34 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s24 (15 kDa, Protein from Neurospora crassa)
- Structure of the translating neurospora crassa ribosome arrested by cycloheximide (Complex)
- 60s ribosomal protein l43 (10 kDa, Protein from Neurospora crassa)
- Mrna (5 kDa, RNA from Neurospora crassa)
- 60s ribosomal protein (14 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l13 (23 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l25 (17 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s23 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s22 (14 kDa, Protein from Neurospora crassa)
- 5s rrna (38 kDa, RNA from Neurospora crassa)
- 40s ribosomal protein s30 (6 kDa, Protein from Neurospora crassa)
- Probable 40s ribosomal protein s10-b (18 kDa, Protein from Neurospora crassa)
- Spermidine (145 Da, Ligand)
Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 7dh5
Q-score: 0.55
Nagiri C, Kobayashi K, Tomita A, Kato M, Kobayashi K, Yamashita K, Nishizawa T, Inoue A, Shihoya W, Nureki O
Mol Cell (2021) 81 pp. 3205-3215.e5 [ Pubmed: 34314699 DOI: doi:10.1016/j.molcel.2021.06.024 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short,guanine nucleotide-binding protein g(s) subunit alpha isoforms short (28 kDa, Protein from Homo sapiens)
- 2-(2-azanyl-1,3-thiazol-4-yl)-n-[4-[2-[[(2r)-2-oxidanyl-2-phenyl-ethyl]amino]ethyl]phenyl]ethanamide (396 Da, Ligand)
- Beta-3 adrenergic receptor (42 kDa, Protein from Canis lupus familiaris)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Dog beta3 adrenergic receptor bound to mirabegron in complex with a minigs heterotrimer (Complex)
- Nanobody nb35 (Complex from unidentified)
- Beta-3 adrenergic receptor (Complex from Canis lupus familiaris)
- Nanobody nb35 (15 kDa, Protein from unidentified)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Rattus norvegicus)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (Complex from Homo sapiens)
Dunaliella Photosystem I Supercomplex
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 6sl5
Q-score: 0.53
Caspy I, Malavath T, Klaiman D, Fadeeva M, Shkolnisky Y, Nelson N
Biochim Biophys Acta Bioenerg (2020) 1861 pp. 148253-148253 [ Pubmed: 32569661 DOI: doi:10.1016/j.bbabio.2020.148253 ]
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Psaf (18 kDa, Protein from Dunaliella salina)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Dunaliella salina)
- Beta-carotene (536 Da, Ligand)
- Psak (8 kDa, Protein from Dunaliella salina)
- Lhca2 (22 kDa, Protein from Dunaliella salina)
- Large dunaliella salina photosystem i-lhc supercomplex (Complex from Dunaliella salina)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (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)
- Psae (7 kDa, Protein from Dunaliella salina)
- Lhca4 (23 kDa, Protein from Dunaliella salina)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Dunaliella salina)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Dunaliella salina)
- Chlorophyll b (907 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Dunaliella salina)
- Lhca6 (19 kDa, Protein from Dunaliella salina)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Octadecanal (268 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Dunaliella salina)
- Psad (16 kDa, Protein from Dunaliella salina)
- Calcium ion (40 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Psao (9 kDa, Protein from Dunaliella salina)
- Phylloquinone (450 Da, Ligand)
- Lhca5 (21 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Dunaliella salina)
- Psal (16 kDa, Protein from Dunaliella salina)
- Psai (4 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- [(2~{r})-1-nonanoyloxy-3-[oxidanyl-[(2~{r},3~{s},5~{r},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{z},8~{z})-heptadeca-5,8-dienoate (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Trimethyl-[(2~{r})-1-oxidanyl-1-oxidanylidene-4-[(2~{s})-2-[(1~{s})-1-oxidanyloctadecoxy]-3-[(1~{r})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium (773 Da, Ligand)
- Psag (10 kDa, Protein from Dunaliella salina)
- Tripalmitoylglycerol (807 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Psah (10 kDa, Protein from Dunaliella salina)
- Chlorophyll a isomer (893 Da, Ligand)
PI(4,5)P2 bound full-length rbTRPV5
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6dmu
Q-score: 0.454
Hughes TET, Pumroy RA, Yazici AT, Kasimova MA, Fluck EC, Huynh KW, Samanta A, Molugu SK, Zhou ZH, Carnevale V, Rohacs T, Moiseenkova-Bell VY
Nat Commun (2018) 9 pp. 4198-4198 [ DOI: doi:10.1038/s41467-018-06753-6 Pubmed: 30305626 ]
- Transient receptor potential cation channel subfamily v member 5 (82 kDa, Protein from Oryctolagus cuniculus)
- Pi(4,5)p2-bound rbtrpv5 (Complex)
- Rbtrpv5 (Complex from Rattus norvegicus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
Cryo-EM structure of the red algal PSI-LHCR
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 5zgb
Q-score: 0.399
Pi X, Tian L, Dai HE, Qin X, Cheng L, Kuang T, Sui SF, Shen JR
PNAS (2018) 115 pp. 4423-4428 [ Pubmed: 29632169 DOI: doi:10.1073/pnas.1722482115 ]
- Lhcr2 (21 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- 1-dodecanol (186 Da, Ligand)
- Psaj (4 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lhcr1 (19 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Psak (6 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Psaa (82 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Lhcr3 (20 kDa, Protein from Cyanidioschyzon merolae strain 10D)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Psab (82 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Psao (16 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Beta-d-glucopyranose (180 Da, Ligand)
- Psi-5lhcr (Complex from Cyanidioschyzon merolae)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Psam (3 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Phylloquinone (450 Da, Ligand)
- Psad (15 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Psai (3 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Chlorophyll a (893 Da, Ligand)
- Psae (10 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Psal (15 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Iron/sulfur cluster (351 Da, Ligand)
- Psac (8 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Psaf (21 kDa, Protein from Cyanidioschyzon merolae (strain 10D))
- Chlorophyll a isomer (893 Da, Ligand)