SIRT6 bound to an H3K9Ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8f86
Q-score: 0.434
Wang ZA, Markert JW, Whedon SD, Yapa Abeywardana M, Lee K, Jiang H, Suarez C, Lin H, Farnung L, Cole PA
J Am Chem Soc (2023) 145 pp. 6811-6822 [ DOI: doi:10.1021/jacs.2c13512 Pubmed: 36930461 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- [(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3ar,5r,6r,6ar)-6-hydroxytetrahydro-2h-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) (587 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Sirt6 bound to h3k9ac (Complex)
- Dna (148-mer) (56 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nad-dependent protein deacylase sirtuin-6 (39 kDa, Protein from Homo sapiens)
- Dna (148-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b6g
Q-score: 0.402
Muhleip A, Flygaard RK, Baradaran R, Haapanen O, Gruhl T, Tobiasson V, Marechal A, Sharma V, Amunts A
Nature (2023) 615 pp. 934-938 [ DOI: doi:10.1038/s41586-023-05817-y Pubmed: 36949187 ]
- Succinate dehydrogenase (quinone) (36 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila)
- Sdhtt3 (23 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (35 kDa, Protein from Tetrahymena thermophila)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Diphthamide synthesis protein (22 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila)
- Sdhtt11 (5 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila)
- Heme c (618 Da, Ligand)
- Nmra domain-containing protein (36 kDa, Protein from Tetrahymena thermophila)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Transmembrane protein, putative (9 kDa, Protein from Tetrahymena thermophila)
- Transposase (11 kDa, Protein from Tetrahymena thermophila)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Duf4885 domain-containing protein (12 kDa, Protein from Tetrahymena thermophila)
- Cytochrome b-c1 complex subunit 8 (7 kDa, Protein from Tetrahymena thermophila)
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (70 kDa, Protein from Tetrahymena thermophila)
- Sdhd (5 kDa, Protein from Tetrahymena thermophila)
- Fe3-s4 cluster (295 Da, Ligand)
- Succinate dehydrogenase complex (complex-ii) (305 kDa, Complex from Tetrahymena thermophila)
- Calcium ion (40 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7tu9
Q-score: 0.521
Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S
Nat Commun (2023) 14 pp. 1363- [ DOI: doi:10.1038/s41467-023-37106-7 ]
- [(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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Strychnine (334 Da, Ligand)
- Glycine receptor beta subunit 2 (65 kDa, Protein from Danio rerio)
- Glycine receptor subunit alphaz1 (52 kDa, Protein from Danio rerio)
- 1,2-dimyristoyl-sn-glycero-3-phosphocholine (678 Da, Ligand)
- Zebrafish alpha1 betab heteromeric glycine receptor (250 kDa, Complex from Danio rerio)
Cryo-EM structure of human NaV1.6/beta1/beta2-4,9-anhydro-tetrodotoxin
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8gz2
Q-score: 0.422
Li Y, Yuan T, Huang B, Zhou F, Peng C, Li X, Qiu Y, Yang B, Zhao Y, Huang Z, Jiang D
Nat Commun (2023) 14 pp. 1030-1030 [ Pubmed: 36823201 DOI: doi:10.1038/s41467-023-36766-9 ]
- (1r,2s,3s,4r,5r,9s,11s,12s,14r)-7-amino-2,4,12-trihydroxy-2-(hydroxymethyl)-10,13,15-trioxa-6,8-diazapentacyclo[7.4.1.1~3,12~.0~5,11~.0~5,14~]pentadec-7-en-8-ium (non-preferred name) (301 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- Sodium channel protein type 8 subunit alpha (225 kDa, Protein from Homo sapiens)
- Structure of human voltage-gated sodium channel nav1.6 in complex with auxiliary beta subunits (Complex from Homo sapiens)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7wsq
Q-score: 0.414
Suzuki Y, Makino F, Miyata T, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O
ACS Catal (2023) 13 pp. 13828-13837 [ DOI: doi:10.1021/acscatal.3c03769 ]
- Fe3-s4 cluster (295 Da, Ligand)
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- D-fructose dehydrogenase from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Fructose dehydrogenase large subunit (59 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)
Resolution: 2.29 Å
EM Method: Single-particle
Fitted PDBs: 8beh
Q-score: 0.711
Klusch N, Dreimann M, Senkler J, Rugen N, Kuhlbrandt W, Braun HP
Nat Plants (2023) 9 pp. 142-156 [ Pubmed: 36585502 DOI: doi:10.1038/s41477-022-01308-6 ]
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- Acyl carrier protein 1, mitochondrial (13 kDa, Protein from Arabidopsis thaliana)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- At1g67350 (11 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (13 kDa, Protein from Arabidopsis thaliana)
- Mitochondrial arabidopsis thaliana i+iii2 supercomplex (ci membrane tip) (Complex from Arabidopsis thaliana)
- Transmembrane protein (9 kDa, Protein from Arabidopsis thaliana)
- Nadh-ubiquinone oxidoreductase chain 5 (74 kDa, Protein from Arabidopsis thaliana)
- Esss subunit of nadh:ubiquinone oxidoreductase (complex i) protein (12 kDa, Protein from Arabidopsis thaliana)
- Nadh-ubiquinone oxidoreductase chain 4 (55 kDa, Protein from Arabidopsis thaliana)
- At2g31490 protein (8 kDa, Protein from Arabidopsis thaliana)
- Water (18 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 (7 kDa, Protein from Arabidopsis thaliana)
- (7s)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-a (8 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (11 kDa, Protein from Arabidopsis thaliana)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (13 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-b (12 kDa, Protein from Arabidopsis thaliana)
- Phosphatidylethanolamine (734 Da, Ligand)
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)
Resolution: 2.25 Å
EM Method: Single-particle
Fitted PDBs: 8bel
Q-score: 0.682
Klusch N, Dreimann M, Senkler J, Rugen N, Kuhlbrandt W, Braun HP
Nat Plants (2023) 9 pp. 142-156 [ Pubmed: 36585502 DOI: doi:10.1038/s41477-022-01308-6 ]
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Cytochrome c1 2, heme protein, mitochondrial (33 kDa, Protein from Arabidopsis thaliana)
- Cytochrome b (44 kDa, Protein from Arabidopsis thaliana)
- Cardiolipin (1 kDa, Ligand)
- Mitochondrial arabidopsis thaliana i+iii2 supercomplex (ciii membrane domain) (Complex from Arabidopsis thaliana)
- Cytochrome b-c1 complex subunit 10, mitochondrial (5 kDa, Protein from Arabidopsis thaliana)
- Cytochrome b-c1 complex subunit 9, mitochondrial (8 kDa, Protein from Arabidopsis thaliana)
- Cytochrome b-c1 complex subunit 6-1, mitochondrial (7 kDa, Protein from Arabidopsis thaliana)
- Water (18 Da, Ligand)
- (7s)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
- Cytochrome b-c1 complex subunit rieske-1, mitochondrial (29 kDa, Protein from Arabidopsis thaliana)
- Ubiquinone-7 (658 Da, Ligand)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
- Cytochrome b-c1 complex subunit 8-1, mitochondrial (8 kDa, Protein from Arabidopsis thaliana)
- Phosphatidylethanolamine (734 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 2,3-dimethoxy-5-methyl-6-(3,11,15,19-tetramethyl-eicosa-2,6,10,14,18-pentaenyl)-[1,4]benzoquinone (522 Da, Ligand)
SsoMCM hexamer bound to Mg/ADP-BeFx and 12-mer oligo-dT. Class 1
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8eaf
Q-score: 0.497
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ssomcm hexamer bound to mg/adp-befx and 12-mer oligo-dt. class 1. (Complex from Saccharolobus solfataricus P2)
- 12-mer oligo dt (3 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
SsoMCM hexamer bound to Mg/ADP-BeFx and 12-mer oligo-dT. Class 2
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8eag
Q-score: 0.432
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 12-mer oligo-dt (3 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Ssomcm hexamer bound to mg/adp-befx and 12-mer oligo-dt. class 2. (Complex from Saccharolobus solfataricus P2)
- Water (18 Da, Ligand)
SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 1
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8eah
Q-score: 0.509
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 16-mer oligo-dt (4 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Ssomcm hexamer bound to mg/adp-befx and 16-mer oligo-dt class 1 (Complex from Saccharolobus solfataricus P2)