Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8oew
Q-score: 0.56
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- 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-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)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- 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)
- Non-template dna (14 kDa, DNA from synthetic construct)
RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- General transcription factor iib (Complex from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Tata-box binding protein (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription factor iia (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein 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)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8byq
Q-score: 0.187
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- General transcription factor iib (Complex from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Tata-box binding protein (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iih (Complex from Homo sapiens)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8bz1
Q-score: 0.244
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- General transcription factor iib (Complex from Homo sapiens)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Tata-box binding protein (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription factor iia (Complex from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Rna polymerase ii core pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- 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)
Structural basis of Integrator-mediated transcription regulation
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7pks
Q-score: 0.278
Fianu I, Chen Y, Dienemann C, Dybkov O, Linden A, Urlaub H, Cramer P
Science (2021) 374 pp. 883-887 [ DOI: doi:10.1126/science.abk0154 Pubmed: 34762484 ]
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Nelf (Complex from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Unknown (2 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Rna (Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Dsif (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Template dna (Complex from Human immunodeficiency virus 1)
- Rpbi c-terminal domain peptide (1 kDa, Protein from Sus scrofa domesticus)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
Overall map of a transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7b0y
Q-score: 0.344
Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P
Science (2021) 371 pp. 305-309 [ Pubmed: 33446560 DOI: doi:10.1126/science.abf1870 ]
- The transcribing rna polymerase ii-u1 snrnp complex with 145-nt rna (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- U1 small nuclear ribonucleoprotein 70 kda (51 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- U1 snrna (52 kDa, RNA from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Nucleic acids (Complex from synthetic construct)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- U1 snrnp (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- U1 small nuclear ribonucleoprotein a (31 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein-associated protein (23 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- 145-nt rna (46 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ted
Q-score: 0.338
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P
Nat Struct Mol Biol (2020) 27 pp. 668-677 [ Pubmed: 32541898 DOI: doi:10.1038/s41594-020-0437-1 ]
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Human transcription factors and associated proteins (Complex from Homo sapiens)
- Dna/rna (Complex from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Uncharacterized protein (13 kDa, Protein from Sus scrofa)
- 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)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna (37-mer) (14 kDa, DNA from synthetic construct)
- Pig dna/rna polymerase subunits (Complex from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 and spt5 (Complex from Homo sapiens)
- Complete ec* (1 MDa, Complex)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (219 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)
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)