Native capsid of Rhodobacter microvirus Ebor computed with I4 symmetry
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ffh
Q-score: 0.456
Bardy P, MacDonald CIW, Kirchberger PC, Jenkins HT, Botka T, Byrom L, Alim NTB, Traore DAK, Konig HC, Nicholas TR, Chechik M, Hart SJ, Turkenburg JP, Blaza JN, Beatty JT, Fogg PCM, Antson AA
bioRxiv (2024) [ DOI: doi:10.1101/2024.06.11.598214 Pubmed: 38915634 ]
- Rhodobacter phage ebor (5 MDa, Virus from Rhodobacter phage Ebor)
- Major capsid protein (55 kDa, Protein from Rhodobacter capsulatus SB 1003)
Bardy P, MacDonald CIW, Kirchberger PC, Jenkins HT, Botka T, Byrom L, Alim NTB, Traore DAK, Konig HC, Nicholas TR, Chechik M, Hart SJ, Turkenburg JP, Blaza JN, Beatty JT, Fogg PCM, Antson AA
bioRxiv (2024) [ DOI: doi:10.1101/2024.06.11.598214 Pubmed: 38915634 ]
R. capsulatus cyt bc1 (CIII2) at 3.3A
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6xi0
Q-score: 0.48
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Homodimer of ubiquinol:cytochrome c reductase (complex iii or cyt bc1 complex) (250 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
R. capsulatus cyt bc1 with both FeS proteins in c position (CIII2 c-c)
Resolution: 3.75 Å
EM Method: Single-particle
Fitted PDBs: 6xkt
Q-score: 0.418
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Homodimer of ubiquinol:cytochrome c reductase (complex iii or cyt bc1 complex) (250 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
R. capsulatus cyt bc1 with one FeS protein in b position and one in c position (CIII2 b-c)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6xku
Q-score: 0.342
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Heme c (618 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Ubiquinol:cytochrome c reductase (complex iii or cyt bc1 complex) (250 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
R. capsulatus cyt bc1 with both FeS proteins in b position (CIII2 b-b)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6xkv
Q-score: 0.444
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Heme c (618 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Ubiquinol:cytochrome c reductase (complex iii or cyt bc1 complex) (250 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy
Resolution: 5.2 Å
EM Method: Single-particle
Fitted PDBs: 6xkw
Q-score: 0.18
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Ciii2civ bipartite super-complex (sc-2a) with ccoh/cy (Complex from Rhodobacter capsulatus SB 1003)
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Copper (ii) ion (63 Da, Ligand)
- Ciii2 (Complex from Rhodobacter capsulatus SB 1003)
- Ccoh/cy (Complex from Rhodobacter capsulatus SB 1003)
- Cbb3-type cytochrome c oxidase subunit ccop (31 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c oxidase, cbb3-type, subunit ii (26 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c oxidase, cbb3-type, biogenesis protein ccoh (16 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c oxidase, cbb3-type, subunit i (58 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c-type cyt cy (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Heme c (618 Da, Ligand)
- Civ (Complex from Rhodobacter capsulatus SB 1003)
R. capsulatus CIII2CIV tripartite super-complex, conformation A (SC-1A)
Resolution: 6.1 Å
EM Method: Single-particle
Fitted PDBs: 6xkx
Q-score: 0.147
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Copper (ii) ion (63 Da, Ligand)
- Ciii2civ tripartite super-complex, conformation a (sc-1a) (Complex from Rhodobacter capsulatus SB 1003)
- Ciii2 (Complex from Rhodobacter capsulatus SB 1003)
- Cytochrome c oxidase, cbb3-type, subunit ii (26 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Civ (Complex from Rhodobacter capsulatus SB 1003)
- Cytochrome c oxidase, cbb3-type, subunit i (58 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cbb3-type cytochrome c oxidase subunit ccop,cytochrome c-type cyt cy (50 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
R. capsulatus CIII2CIV tripartite super-complex, conformation B (SC-1B)
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 6xkz
Q-score: 0.122
Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F
Nat Commun (2021) 12 pp. 929-929 [ Pubmed: 33568648 DOI: doi:10.1038/s41467-021-21051-4 ]
- Cytochrome b (49 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cytochrome c1 (30 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Copper (ii) ion (63 Da, Ligand)
- Ciii2civ tripartite super-complex, conformation b (sc-1b) (Complex from Rhodobacter capsulatus SB 1003)
- Ciii2 (Complex from Rhodobacter capsulatus SB 1003)
- Cytochrome c oxidase, cbb3-type, subunit ii (26 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Civ (Complex from Rhodobacter capsulatus SB 1003)
- Cytochrome c oxidase, cbb3-type, subunit i (58 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
- Cbb3-type cytochrome c oxidase subunit ccop,cytochrome c-type cyt cy (50 kDa, Protein from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Resolution: 10.47 Å
EM Method: Single-particle
Fitted PDBs: 6tui
Q-score: 0.08
Bardy P, Fuzik T, Hrebik D, Pantucek R, Beatty JT, Plevka P
Nat Commun (2020) 11 pp. 3034- [ DOI: doi:10.1038/s41467-020-16669-9 Pubmed: 32541663 ]
- Connector (760 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Tail (730 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (9 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Tail terminator protein rcc01690 (13 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Portal protein rcc01684 (42 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Head spike (80 kDa, Complex from Rhodobacter capsulatus SB 1003)
- Phage major capsid protein, hk97 family (40 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Uncharacterized protein (32 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Rhodobacter capsulatus de442 (8 MDa, Virus)
- Capsid (5 MDa, Complex from Rhodobacter capsulatus SB 1003)
- Tail tube protein rcc01691 (14 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Adaptor protein rcc01688 (20 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Stopper protein rcc01689 (12 kDa, Protein from Rhodobacter capsulatus SB 1003)