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 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 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 ]
- Unknown (2 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Rpbi c-terminal domain peptide (1 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Dsif (Complex from Homo sapiens)
- Nelf (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna (Complex from Human immunodeficiency virus 1)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Template dna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
SARS-CoV-2 S (Spike) protein in complex with VHH Re5D06 (multi-body-refined RBD-Re5D06 body)
Guttler T, Aksu M, Dickmanns A, Stegmann KM, Gregor K, Rees R, Taxer W, Rymarenko O, Schunemann J, Dienemann C, Gunkel P, Mussil B, Krull J, Teichmann U, Gross U, Cordes VC, Dobbelstein M, Gorlich D
EMBO J (2021) 40 pp. e107985-e107985 [ Pubmed: 34302370 DOI: doi:10.15252/embj.2021107985 ]
- Sars-cov-2 hexapro s (spike) glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Vhh re5d06 (Protein from Vicugna pacos)
- Sars-cov-2 hexapro s (spike) glycoprotein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 hexapro s (spike) glycoprotein in complex with neutralizing vhh re5d06 (Complex)
- Vhh re5d06 (14 MDa, Complex from Vicugna pacos)
SARS-CoV-2 S (Spike) protein in complex with VHH Re5D06 (one RBD down)
Guttler T, Aksu M, Dickmanns A, Stegmann KM, Gregor K, Rees R, Taxer W, Rymarenko O, Schunemann J, Dienemann C, Gunkel P, Mussil B, Krull J, Teichmann U, Gross U, Cordes VC, Dobbelstein M, Gorlich D
EMBO J (2021) 40 pp. e107985-e107985 [ Pubmed: 34302370 DOI: doi:10.15252/embj.2021107985 ]
- Sars-cov-2 hexapro s (spike) glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Vhh re5d06 (Protein from Vicugna pacos)
- Sars-cov-2 hexapro s (spike) glycoprotein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 hexapro s (spike) glycoprotein in complex with neutralizing vhh re5d06 (Complex)
- Vhh re5d06 (14 MDa, Complex from Vicugna pacos)
SARS-CoV-2 S (Spike) protein in complex with VHH Re5D06 (all RBDs up)
Guttler T, Aksu M, Dickmanns A, Stegmann KM, Gregor K, Rees R, Taxer W, Rymarenko O, Schunemann J, Dienemann C, Gunkel P, Mussil B, Krull J, Teichmann U, Gross U, Cordes VC, Dobbelstein M, Gorlich D
EMBO J (2021) 40 pp. e107985-e107985 [ Pubmed: 34302370 DOI: doi:10.15252/embj.2021107985 ]
- Sars-cov-2 hexapro s (spike) glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Vhh re5d06 (Protein from Vicugna pacos)
- Sars-cov-2 hexapro s (spike) glycoprotein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 hexapro s (spike) glycoprotein in complex with neutralizing vhh re5d06 (Complex)
- Vhh re5d06 (14 MDa, Complex from Vicugna pacos)