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 ]
Rhodobacter microvirus Ebor attached to the outer membrane vesicle
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 microvirus Ebor attached to the host cell reconstructed by subtomogram averaging
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 ]
Iron Nitrogenase Complex from Rhodobacter capsulatus
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8oie
Q-score: 0.666
Schmidt FV, Schulz L, Zarzycki J, Prinz S, Oehlmann NN, Erb TJ, Rebelein JG
Nat Struct Mol Biol (2024) 31 pp. 150-158 [ Pubmed: 38062208 DOI: doi:10.1038/s41594-023-01124-2 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Nitrogenase protein alpha chain (60 kDa, Protein from Rhodobacter capsulatus SB 1003)
- 3-hydroxy-3-carboxy-adipic acid (206 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Nitrogenase iron protein (30 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Fe(8)-s(7) cluster (671 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Fefe cofactor (747 Da, Ligand)
- Nitrogenase iron-iron protein delta chain (13 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Aluminum fluoride (83 Da, Ligand)
- Nitrogenase iron-iron protein, beta subunit (50 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Iron nitrogenase complex from rhodobacter capsulatus (360 kDa, Complex from Rhodobacter capsulatus SB 1003)
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8pbb
Q-score: 0.655
Schmidt FV, Schulz L, Zarzycki J, Prinz S, Oehlmann NN, Erb TJ, Rebelein JG
Nat Struct Mol Biol (2024) 31 pp. 150-158 [ Pubmed: 38062208 DOI: doi:10.1038/s41594-023-01124-2 ]
- Fe(8)-s(7) cluster (671 Da, Ligand)
- Nitrogenase iron-iron protein, beta subunit (50 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Nitrogenase protein alpha chain (60 kDa, Protein from Rhodobacter capsulatus SB 1003)
- Chapso treated partial catalytic component (comprising only anfd & anfk, lacking anfg and fefeco) of iron nitrogenase from rhodobacter capsulatus (Complex from Rhodobacter capsulatus SB 1003)
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))