Porcine epidemic diarrhea virus core polymerase complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8g6r
Q-score: 0.435
Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN
bioRxiv (2023) [ DOI: doi:10.1101/2023.03.15.532841 Pubmed: 36993498 ]
- Nsp7 (6 kDa, Protein from Porcine epidemic diarrhea virus)
- Core replication complex of porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short rna substrate (185 kDa, Complex from Porcine epidemic diarrhea virus)
- Nsp12 (104 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (5'-r(p*gp*gp*up*up*gp*up*gp*ap*up*up*up*up*ap*ap*up*ap*gp*cp*up*u)-3') (6 kDa, RNA from synthetic construct)
- Nsp8 (12 kDa, Protein from Porcine epidemic diarrhea virus)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*ap*ap*gp*ap*ap*gp*cp*up*ap*up*up*ap*ap*ap*ap*up*cp*ap*cp*a)-3') (6 kDa, RNA from synthetic construct)
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8cx0
Q-score: 0.509
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
Nature (2023) 615 pp. 728-733 [ Pubmed: 36754086 DOI: doi:10.1038/s41586-023-05779-1 ]
- Rna (5'-r(p*ap*ap*ap*ap*ap*ap*ap*a)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Virion infectivity factor (22 kDa, Protein from Human immunodeficiency virus 1)
- Dna dc->du-editing enzyme apobec-3g (50 kDa, Protein from Homo sapiens)
- Hiv-1 vif-e3 ligase substrate receptor (vcbc) in complex with human apobec3g and rna (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Core-binding factor subunit beta (21 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8cx1
Q-score: 0.366
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
Nature (2023) 615 pp. 728-733 [ Pubmed: 36754086 DOI: doi:10.1038/s41586-023-05779-1 ]
- Virion infectivity factor (22 kDa, Protein from Human immunodeficiency virus 1)
- Dna dc->du-editing enzyme apobec-3g (50 kDa, Protein from Homo sapiens)
- Hiv-1 vif-e3 ligase substrate receptor (vcbc) in complex with human apobec3g and rna (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Core-binding factor subunit beta (21 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*ap*ap*ap*up*ap*up*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*ap*ap*ap*up*ap*up*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8cx2
Q-score: 0.375
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
Nature (2023) 615 pp. 728-733 [ Pubmed: 36754086 DOI: doi:10.1038/s41586-023-05779-1 ]
- Virion infectivity factor (22 kDa, Protein from Human immunodeficiency virus 1)
- Dna dc->du-editing enzyme apobec-3g (50 kDa, Protein from Homo sapiens)
- Hiv-1 vif-e3 ligase substrate receptor (vcbc) in complex with human apobec3g and rna (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Core-binding factor subunit beta (21 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*ap*up*ap*ap*ap*ap*ap*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*up*up*ap*ap*ap*ap*ap*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)
Resolution: 2.04 Å
EM Method: Single-particle
Fitted PDBs: 8bee
Q-score: 0.749
Klusch N, Dreimann M, Senkler J, Rugen N, Kuhlbrandt W, Braun HP
Nat Plants (2023) 9 pp. 142-156 [ DOI: doi:10.1038/s41477-022-01308-6 Pubmed: 36585502 ]
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 3 (22 kDa, Protein from Arabidopsis thaliana)
- Probable nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial (19 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-a (16 kDa, Protein from Arabidopsis thaliana)
- Water (18 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (24 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (15 kDa, Protein from Arabidopsis thaliana)
- Probable nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (18 kDa, Protein from Arabidopsis thaliana)
- Iron/sulfur cluster (351 Da, Ligand)
- Mitochondrial arabidopsis thaliana i+iii2 supercomplex (ci peripheral core) (Complex from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 8-a, mitochondrial (25 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase subunit 7 (45 kDa, Protein from Arabidopsis thaliana)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (43 kDa, Protein from Arabidopsis thaliana)
- Acyl carrier protein 2, mitochondrial (14 kDa, Protein from Arabidopsis thaliana)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
CryoEM structure of sNS1 complexed with Fab5E3
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7wur
Q-score: 0.427
Shu B, Ooi JSG, Tan AWK, Ng TS, Dejnirattisai W, Mongkolsapaya J, Fibriansah G, Shi J, Kostyuchenko VA, Screaton GR, Lok SM
Nat Commun (2022) 13 pp. 6756-6756 [ DOI: doi:10.1038/s41467-022-34415-1 Pubmed: 36347841 ]
- Dengue ns1 (Complex from Homo sapiens)
- Structure of dengue ns1 complexed with fab 5e3 (Complex from Dengue virus 2)
- Fab 5e3 heavy chain (12 kDa, Protein from Homo sapiens)
- Fab 5e3 (Complex)
- Fab 5e3 light chain (11 kDa, Protein from Homo sapiens)
- Core protein (38 kDa, Protein from Dengue virus 2)
CryoEM structure of stable sNS1 tetramer
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7wut
Q-score: 0.368
Shu B, Ooi JSG, Tan AWK, Ng TS, Dejnirattisai W, Mongkolsapaya J, Fibriansah G, Shi J, Kostyuchenko VA, Screaton GR, Lok SM
Nat Commun (2022) 13 pp. 6756-6756 [ DOI: doi:10.1038/s41467-022-34415-1 Pubmed: 36347841 ]
CryoEM structure of loose sNS1 tetramer
Resolution: 8.3 Å
EM Method: Single-particle
Fitted PDBs: 7wuu
Q-score: 0.101
Shu B, Ooi JSG, Tan AWK, Ng TS, Dejnirattisai W, Mongkolsapaya J, Fibriansah G, Shi J, Kostyuchenko VA, Screaton GR, Lok SM
Nat Commun (2022) 13 pp. 6756-6756 [ DOI: doi:10.1038/s41467-022-34415-1 Pubmed: 36347841 ]
CryoEM structure of sNS1 hexamer
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7wuv
Q-score: 0.055
Shu B, Ooi JSG, Tan AWK, Ng TS, Dejnirattisai W, Mongkolsapaya J, Fibriansah G, Shi J, Kostyuchenko VA, Screaton GR, Lok SM
Nat Commun (2022) 13 pp. 6756-6756 [ DOI: doi:10.1038/s41467-022-34415-1 Pubmed: 36347841 ]
- Ns1 hexamer (Cellular component from Dengue virus 2)
- Core protein (34 kDa, Protein from Dengue virus 2)
Cryo-EM structure of the core human NADPH oxidase NOX2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7u8g
Q-score: 0.54
Noreng S, Ota N, Sun Y, Ho H, Johnson M, Arthur CP, Schneider K, Lehoux I, Davies CW, Mortara K, Wong K, Seshasayee D, Masureel M, Payandeh J, Yi T, Koerber JT
Nat Commun (2022) 13 pp. 6079-6079 [ DOI: doi:10.1038/s41467-022-33711-0 Pubmed: 36241643 ]
- 7g5 - heavy chain (23 kDa, Protein from Oryctolagus cuniculus)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Cytochrome b-245 light chain (21 kDa, Protein from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Nox2 core - fab 7g5 complex (Complex from Homo sapiens)
- 7g5 - light chain (23 kDa, Protein from Oryctolagus cuniculus)
- Egfp, cytochrome b-245 heavy chain chimera (97 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)