Backbone model of de novo-designed chlorophyll-binding nanocage O32-15
Resolution: 6.5 Å
EM Method: Single-particle
Fitted PDBs: 8glt
Q-score: 0.213
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D
Nat Chem Biol (2024) 20 pp. 906-915 [ Pubmed: 38831036 DOI: doi:10.1038/s41589-024-01626-0 ]
Chlorophyll-binding region of de novo-designed nanocage O32-15
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D
Nat Chem Biol (2024) 20 pp. 906-915 [ Pubmed: 38831036 DOI: doi:10.1038/s41589-024-01626-0 ]
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8asi
Q-score: 0.564
Swainsbury DJK, Hawkings FR, Martin EC, Musial S, Salisbury JH, Jackson PJ, Farmer DA, Johnson MP, Siebert CA, Hitchcock A, Hunter CN
PNAS (2023) 120 pp. e2217922120-e2217922120 [ Pubmed: 36913593 DOI: doi:10.1073/pnas.2217922120 ]
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (19 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b (50 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Four subunit cytochrome b-c1 complex from rhodobacter sphaeroides (Complex from Cereibacter sphaeroides)
- Cytochrome b-c1 subunit iv (14 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Cytochrome c1 (30 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Resolution: 3.75 Å
EM Method: Single-particle
Fitted PDBs: 8asj
Q-score: 0.504
Swainsbury DJK, Hawkings FR, Martin EC, Musial S, Salisbury JH, Jackson PJ, Farmer DA, Johnson MP, Siebert CA, Hitchcock A, Hunter CN
PNAS (2023) 120 pp. e2217922120-e2217922120 [ Pubmed: 36913593 DOI: doi:10.1073/pnas.2217922120 ]
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (19 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b (50 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Four subunit cytochrome b-c1 complex from rhodobacter sphaeroides (Complex from Cereibacter sphaeroides)
- Cytochrome b-c1 subunit iv (14 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Cytochrome c1 (30 kDa, Protein from Cereibacter sphaeroides 2.4.1)
PucA-LH2 complex from Rps. palustris
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7zcu
Q-score: 0.612
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ Pubmed: 36251992 DOI: doi:10.1073/pnas.2210109119 ]
- 1,2-dihydro-psi,psi-caroten-1-ol (554 Da, Ligand)
- Water (18 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Light-harvesting protein b-800-850 beta chain (5 kDa, Protein from Rhodopseudomonas palustris ATCC 17001)
- Light-harvesting protein b-800-850 alpha chain (6 kDa, Protein from Rhodopseudomonas palustris ATCC 17001)
- Puca-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris ATCC 17001)
PucB-LH2 complex from Rps. palustris
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7zdi
Q-score: 0.607
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ Pubmed: 36251992 DOI: doi:10.1073/pnas.2210109119 ]
- Light-harvesting protein (6 kDa, Protein from Rhodopseudomonas palustris)
- 1,2-dihydro-psi,psi-caroten-1-ol (554 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris)
- Pucb-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Light-harvesting protein (5 kDa, Protein from Rhodopseudomonas palustris)
PucD-LH2 complex from Rps. palustris
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7ze3
Q-score: 0.614
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ Pubmed: 36251992 DOI: doi:10.1073/pnas.2210109119 ]
- Pucd-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Water (18 Da, Ligand)
- Light-harvesting protein b-800-850 alpha chain (6 kDa, Protein from Rhodopseudomonas palustris)
- Bacteriochlorophyll a (911 Da, Ligand)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris)
- Light-harvesting protein b-800-850 beta chain (5 kDa, Protein from Rhodopseudomonas palustris)
- (3'e)-3',4'-didehydro-1,2-dihydro-psi,psi-caroten-1-ol (552 Da, Ligand)
PucE-LH2 complex from Rps. palustris
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ze8
Q-score: 0.509
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ Pubmed: 36251992 DOI: doi:10.1073/pnas.2210109119 ]
- 1,2-dihydro-psi,psi-caroten-1-ol (554 Da, Ligand)
- Light-harvesting protein (6 kDa, Protein from Rhodopseudomonas palustris)
- Bacteriochlorophyll a (911 Da, Ligand)
- Puce-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris)
- Light-harvesting protein (5 kDa, Protein from Rhodopseudomonas palustris)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7r0w
Q-score: 0.523
Proctor MS, Malone LA, Farmer DA, Swainsbury DJK, Hawkings FR, Pastorelli F, Emrich-Mills TZ, Siebert CA, Hunter CN, Johnson MP, Hitchcock A
Biochem J (2022) 479 pp. 1487-1503 [ Pubmed: 35726684 DOI: doi:10.1042/BCJ20220124 ]
- Cytochrome b6-f complex subunit 4 (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Cytochrome f (35 kDa, Protein from Synechocystis sp. PCC 6803)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b6 (25 kDa, Protein from Synechocystis sp. PCC 6803)
- Uncharacterized protein cp097, conserved in cyanobacteria (7 kDa, Protein from Synechocystis)
- Cytochrome b6-f complex subunit 5 (4 kDa, Protein from Synechocystis sp. PCC 6803)
- (4s,7r)-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 b6-f complex subunit 7 (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b6 (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- (1s,8e)-1-{[(2s)-1-hydroxy-3-{[(1s)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol (570 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome b6f complex in association with petp (Complex from Synechocystis sp. PCC 6803)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Eicosane (282 Da, Ligand)
- Cytochrome b6-f complex subunit 8 (3 kDa, Protein from Synechocystis sp. PCC 6803)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Rieske domain, petc (20 kDa, Protein from Synechocystis sp. PCC 6803)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7zxy
Q-score: 0.54
Proctor MS, Malone LA, Farmer DA, Swainsbury DJK, Hawkings FR, Pastorelli F, Emrich-Mills TZ, Siebert CA, Hunter CN, Johnson MP, Hitchcock A
Biochem J (2022) 479 pp. 1487-1503 [ Pubmed: 35726684 DOI: doi:10.1042/BCJ20220124 ]
- Cytochrome f (30 kDa, Protein from Synechocystis sp. PCC 6803)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b6-f complex subunit 5 (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Chlorophyll a (893 Da, Ligand)
- Cytochrome b6-f complex subunit 4 (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Eicosane (282 Da, Ligand)
- Cytochrome b6-f complex iron-sulfur subunit 2 (19 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b6-f complex subunit 8 (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b6 (25 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b6 (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Cytochrome b6f with natively associated lipids and plastoquinone (Complex from Synechocystis sp. PCC 6803)
- Heme c (618 Da, Ligand)
- Cytochrome b6-f complex subunit 7 (3 kDa, Protein from Synechocystis sp. PCC 6803)