The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2, B1, B2)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7z8i
Q-score: 0.466
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (130 kDa, Complex)
- Bicdr1 (Cellular component from Mus musculus)
- Dynactin (Cellular component from Sus scrofa)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein 1 intermediate chain 2 (71 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Dynein, cytoplasmic 1 (Cellular component from Homo sapiens)
- Capping protein (actin filament) muscle z-line, alpha 1 (33 kDa, Protein from Sus scrofa)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- F-actin capping protein beta subunit (30 kDa, Protein from Sus scrofa)
Composite structure of dynein-dynactin-BICDR on microtubules
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 7z8f
Q-score: 0.215
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynactin subunit 4 (52 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- F-actin capping protein beta subunit (30 kDa, Protein from Sus scrofa)
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (4 MDa, Complex)
- Dynactin subunit 3 (21 kDa, Protein from Sus scrofa)
- Dynactin subunit 1 (142 kDa, Protein from Sus scrofa)
- Bicdr1 (130 kDa, Cellular component from Mus musculus)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Capping protein (actin filament) muscle z-line, alpha 1 (33 kDa, Protein from Sus scrofa)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Actin, cytoplasmic 1 (41 kDa, Protein from Sus scrofa)
- Arp11 (46 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (44 kDa, Protein from Sus scrofa)
- Dynactin 6 (20 kDa, Protein from Sus scrofa)
- Dynein light chain roadblock-type 1 (10 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- Dynactin (1 MDa, Cellular component from Sus scrofa)
- Cytoplasmic dynein 1 intermediate chain 2 (71 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Dynactin subunit 5 (20 kDa, Protein from Sus scrofa)
Cytoplasmic dynein-1 motor domain AAA1, AAA2, and AAA3 subunits
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 7z8h
Q-score: 0.497
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Magnesium ion (24 Da, Ligand)
- Bicdr1 (130 kDa, Cellular component from Mus musculus)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (4 MDa, Complex)
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Dynactin (1 MDa, Cellular component from Sus scrofa)
Cytoplasmic dynein (A2) bound to BICDR1
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7z8j
Q-score: 0.364
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Bicdr1 (Cellular component from Mus musculus)
- Dynactin (Cellular component from Sus scrofa)
- Cytoplasmic dynein 1 intermediate chain 2 (71 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- Complex of cytoplasmic dynein (a2) bound to bicdr1 (Complex)
Cytoplasmic dynein (A1) bound to BICDR1
Resolution: 4.37 Å
EM Method: Single-particle
Fitted PDBs: 7z8k
Q-score: 0.29
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein 1 intermediate chain 2 (63 kDa, Protein from Homo sapiens)
- Bicdr1 (130 kDa, Cellular component from Mus musculus)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (4 MDa, Complex)
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Dynactin (1 MDa, Cellular component from Sus scrofa)
Cytoplasmic dynein light intermediate chain (B1) bound to the motor domain (A2).
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 7z8l
Q-score: 0.337
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Magnesium ion (24 Da, Ligand)
- Bicdr1 (130 kDa, Cellular component from Mus musculus)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (4 MDa, Complex)
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Dynactin (1 MDa, Cellular component from Sus scrofa)
The pointed end complex of dynactin bound to BICDR1
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 7z8m
Q-score: 0.511
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Magnesium ion (24 Da, Ligand)
- Dynactin 6 (20 kDa, Protein from Sus scrofa)
- Bicdr1 (130 kDa, Cellular component from Mus musculus)
- Dynactin subunit 2 (44 kDa, Protein from Sus scrofa)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynactin subunit 4 (52 kDa, Protein from Sus scrofa)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynactin subunit 5 (20 kDa, Protein from Sus scrofa)
- Arp11 (46 kDa, Protein from Sus scrofa)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (4 MDa, Complex)
- Zinc ion (65 Da, Ligand)
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Dynactin (1 MDa, Cellular component from Sus scrofa)
- Actin, cytoplasmic 1 (41 kDa, Protein from Sus scrofa)
Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7oob
Q-score: 0.566
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Dna excision repair protein ercc-6 and ercc-8, dna damage-binding protein 1 (Complex from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Complex between the transcribing rna polymerase ii and tcr factors in the presence of adp-bef3. (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna (3 kDa, RNA from Homo sapiens)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opc
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Ts (14 kDa, DNA from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Nts, rna, ts (Complex from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7oo3
Q-score: 0.521
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Rna polymerase ii elongation complex with csb, csa-ddb1 and uvssa. (Complex)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Csb element (2 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna repair proteins, csb element and scaffold protein (Complex from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Nts, ts & rna (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna directed rna polymerase (Complex from Sus scrofa)
- Rna (3 kDa, RNA from Homo sapiens)