The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 7rd1
Q-score: 0.48
Baker AT, Boyd RJ, Sarkar D, Teijeira-Crespo A, Chan CK, Bates E, Waraich K, Vant J, Wilson E, Truong CD, Lipka-Lloyd M, Fromme P, Vermaas J, Williams D, Machiesky L, Heurich M, Nagalo BM, Coughlan L, Umlauf S, Chiu PL, Rizkallah PJ, Cohen TS, Parker AL, Singharoy A, Borad MJ
Sci Adv (2021) 7 pp. eabl8213-eabl8213 [ DOI: doi:10.1126/sciadv.abl8213 Pubmed: 34851659 ]
- Chimpanzee adenovirus y25 (Virus from Chimpanzee adenovirus Y25)
- Hexon protein (106 kDa, Protein from Chimpanzee adenovirus Y25)
- Hexon-interlacing protein (14 kDa, Protein from Chimpanzee adenovirus Y25)
- Penton protein (59 kDa, Protein from Chimpanzee adenovirus Y25)
- Pre-hexon-linking protein viii (24 kDa, Protein from Chimpanzee adenovirus Y25)
- Pre-protein vi (26 kDa, Protein from Chimpanzee adenovirus Y25)
- Pre-hexon-linking protein iiia (65 kDa, Protein from Chimpanzee adenovirus Y25)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6m0r
Q-score: 0.467
Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W
Sci Adv (2020) 6 [ Pubmed: 33028525 DOI: doi:10.1126/sciadv.abb9605 ]
- V-type proton atpase vo sub-complex (400 MDa, Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Uncharacterized protein ypr170w-b (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pyrophosphate (177 Da, Ligand)
- (6~{e},10~{e},14~{e},18~{e},22~{e},26~{e},30~{r})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene (548 Da, Ligand)
- Water (18 Da, Ligand)
- V0 assembly protein 1 (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit a, vacuolar isoform (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c'' (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6m0s
Q-score: 0.384
Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W
Sci Adv (2020) 6 [ Pubmed: 33028525 DOI: doi:10.1126/sciadv.abb9605 ]
- V-type proton atpase vo sub-complex (400 MDa, Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Uncharacterized protein ypr170w-b (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V0 assembly protein 1 (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit a, vacuolar isoform (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c'' (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6pv6
Q-score: 0.18
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Ryanodine receptor 1 (502 kDa, Protein from Oryctolagus cuniculus)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7jmf
Q-score: 0.11
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Ryanodine receptor 1 (502 kDa, Protein from Oryctolagus cuniculus)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7jmg
Q-score: 0.155
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor type 1 (502 kDa, Protein from Oryctolagus cuniculus)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7jmh
Q-score: 0.132
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor type 1 (502 kDa, Protein from Oryctolagus cuniculus)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7jmi
Q-score: 0.153
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor type 1 (502 kDa, Protein from Oryctolagus cuniculus)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7jmj
Q-score: 0.133
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor type 1 (502 kDa, Protein from Oryctolagus cuniculus)