Structure of LINE-1 ORF2p with template:primer hybrid
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8sxt
Q-score: 0.339
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Dna primer (3 kDa, DNA from synthetic construct)
- Rna template (5 kDa, RNA from synthetic construct)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
Structure of LINE-1 ORF2p with an oligo(A) template
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8sxu
Q-score: 0.185
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Rna (25-mer) (8 kDa, RNA from synthetic construct)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7k01
Q-score: 0.331
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ DOI: doi:10.1038/s41467-021-23684-x Pubmed: 34099686 ]
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ternary complex of tfiih/rad4-rad23-rad33 with aaf damaged dna (420 MDa, Complex)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening
Resolution: 9.25 Å
EM Method: Single-particle
Fitted PDBs: 7k04
Q-score: 0.122
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ DOI: doi:10.1038/s41467-021-23684-x Pubmed: 34099686 ]
- Damaged dna strand (8 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Undamaged dna strand (8 kDa, DNA from synthetic construct)
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna repair protein rad33 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- 10 component complex of rad4-23, rad33 and tfiih on damaged dna (Complex)
- Dna repair protein rad4 (87 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Calcium ion (40 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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))