Structure of paused transcription complex Pol II-DSIF-NELF
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6gml
Q-score: 0.34
Vos SM, Farnung L, Urlaub H, Cramer P
Nature (2018) 560 pp. 601-606 [ Pubmed: 30135580 DOI: doi:10.1038/s41586-018-0442-2 ]
- Template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Rna polymerase ii elongation complex bound to dsif and nelf (927 kDa, Complex)
- Negative elongation factor e,negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Hiv-1 pause transcription scaffold (Complex from Human immunodeficiency virus 1)
- Uncharacterized protein (13 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Tar rna (14 kDa, RNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b,negative elongation factor b (64 kDa, Protein from Homo sapiens)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Negative elongation factor c/d (64 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit c (30 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Drb sensitivity inducing factor (dsif) (Complex from Human immunodeficiency virus 1)
- Sus scrofa rna polymerase ii (Complex from Sus scrofa)
- Rna polymerase ii subunit g (19 kDa, Protein from Sus scrofa)
Structure of activated transcription complex Pol II-DSIF-PAF-SPT6 (Map A)
Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P
Nature (2018) 560 pp. 607-612 [ Pubmed: 30135578 DOI: doi:10.1038/s41586-018-0440-4 ]
- Cdc73 (1 kDa, Protein from Homo sapiens)
- Paf1,rna polymerase ii-associated factor 1 homolog,rna polymerase ii-associated factor 1 homolog (67 kDa, Protein from Homo sapiens)
- Leo1,leo1,rna polymerase-associated protein leo1 (84 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Rna polymerase ii-dsif-paf-spt6 elongation complex (ec*) (1 MDa, Complex)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Nucleic acids (Complex from synthetic construct)
- Rna (14 kDa, RNA from synthetic construct)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Ctr9,rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein ctr9 homolog (125 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Associated proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6,transcription elongation factor spt6,transcription elongation factor spt6 (198 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit g (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit c (31 kDa, Protein from Sus scrofa)
Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6f1t
Q-score: 0.269
Urnavicius L, Lau CK, Elshenawy MM, Morales-Rios E, Motz C, Yildiz A, Carter AP
Nature (2018) 554 pp. 202-206 [ Pubmed: 29420470 DOI: doi:10.1038/nature25462 ]
- Dynactin subunit 2 (50 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cytoplasmic dynein 1 heavy chain 1,cytoplasmic dynein 1 heavy chain 1,cytoplasmic dynein 1 heavy chain 1,dynein heavy chain,cytoplasmic dynein 1 heavy chain 1,cytoplasmic dynein 1 heavy chain 1,cytoplasmic dynein 1 heavy chain 1,cytoplasmic dynein 1 heavy chain 1,dynein heavy chain,cytoplasmic dynein 1 heavy chain 1,cytoplasmic dynein 1 heavy chain 1 (119 kDa, Protein from Homo sapiens)
- F-actin capping protein beta subunit (30 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (10 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (52 kDa, Protein from Sus scrofa)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Capping protein (actin filament) muscle z-line, alpha 1 (33 kDa, Protein from Sus scrofa)
- Bicd family-like cargo adapter 1,bicd family-like cargo adapter 1,bicd family-like cargo adapter 1 (42 kDa, Protein from Mus musculus)
- Dynactin subunit 4 (22 kDa, Protein from Sus scrofa)
- Actin, cytoplasmic 1 (41 kDa, Protein from Sus scrofa)
- Dynactin (Complex from Sus scrofa)
- Cryo-em map of two dynein tail domains bound to dynactin and bicdr1 (Complex)
- Dynactin 6 (20 kDa, Protein from Sus scrofa)
- Dynein light chain roadblock-type 1 (10 kDa, Protein from Homo sapiens)
- Dynactin subunit 2 (7 kDa, Protein from Sus scrofa)
- Dynactin subunit 1 (4 kDa, Protein from Sus scrofa)
- Cytoplasmic dynein 1 intermediate chain 2 (68 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Dynactin subunit 1 (4 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (5 kDa, Protein from Sus scrofa)
- Dynactin subunit 3 (5 kDa, Protein from Sus scrofa)
- Bicd family-like cargo adapter 1 (Complex from Mus musculus)
- Actin related protein 10 homolog (43 kDa, Protein from Sus scrofa)
- Bicd family-like cargo adapter 1,bicd family-like cargo adapter 1,bicd family-like cargo adapter 1,bicdr-1 (42 kDa, Protein from Mus musculus)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (7 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (2 kDa, Protein from Sus scrofa)
- Dynein (Complex from Homo sapiens)
- Dynactin subunit 5 (20 kDa, Protein from Sus scrofa)
N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6f1u
Q-score: 0.374
Urnavicius L, Lau CK, Elshenawy MM, Morales-Rios E, Motz C, Yildiz A, Carter AP
Nature (2018) 554 pp. 202-206 [ Pubmed: 29420470 DOI: doi:10.1038/nature25462 ]
- Bicdr1 (Complex from Mus musculus)
- Dynactin filament (Complex from Sus scrofa)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Pig)
- Cytoplasmic dynein 1 heavy chain 1 (136 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein (Complex from Homo sapiens)
- F-actin capping protein beta subunit (30 kDa, Protein from Pig)
- Capping protein (actin filament) muscle z-line, alpha 1 (33 kDa, Protein from Pig)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cytoplasmic dynein 1 intermediate chain 2 (68 kDa, Protein from Homo sapiens)
- Dynactin subunit 2 (2 kDa, Protein from Pig)
- Two dynein tail domains bound to dynactin and bicdr1. (Complex)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- Dynactin subunit 2 (5 kDa, Protein from Pig)