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SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 7ns6
Q-score: 0.372
Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hallberg BM, Murrell B, McInerney GM
Nat Commun (2022) 13 pp. 155-155 [ DOI: doi:10.1038/s41467-021-27610-z Pubmed: 35013189 ]
- Fu2 nanobody (15 kDa, Protein from Vicugna pacos)
- Fu2 nanobody (Complex from Vicugna pacos)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- Sars-cov-2 spike, fibritin (Complex from Enterobacteria phage T4)
- Spike rbd (two molecules) in complex with two fu2 nanobodies (95 kDa, Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 [ Pubmed: 34762484 DOI: doi:10.1126/science.abk0154 ]
- Dsif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from domestic pig)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from domestic pig)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from domestic pig)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from domestic pig)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from domestic pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from domestic pig)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Template dna (Complex from Human immunodeficiency virus 1)
- Unknown (2 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Rpbi c-terminal domain peptide (1 kDa, Protein from domestic pig)
- Rna (Complex from Human immunodeficiency virus 1)
- Nelf (Complex from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from domestic pig)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from domestic pig)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Manganese (ii) ion (54 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from domestic pig)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from domestic pig)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from domestic pig)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from domestic pig)
ATPgS bound TnsC filament from shCAST system
Resolution: 3.2 Å
EM Method: Helical reconstruction
Fitted PDBs: 7m99
Q-score: 0.477
Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH
Science (2021) 373 pp. 768-774 [ Pubmed: 34385391 DOI: doi:10.1126/science.abi8976 ]
- Helical filament of tnsc monomers bound to dna (45 MDa, Complex from Scytonema hofmannii)
- Tnsc (31 kDa, Protein from Scytonema hofmannii)
- Dna (5'-d(p*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (6 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (6 kDa, DNA from synthetic construct)
ATP bound TnsC filament structure from ShCAST system
Park J, Tsai A, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH
Science (2021) [ DOI: doi:10.1126/science.abi8976 ]
- Tnsc (Protein from Scytonema hofmannii)
- Helical filament of tnsc monomers bound to dna (45 MDa, Complex from Scytonema hofmannii)
Head-to-head filament of TnsC from ShCAST system
Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH
Science (2021) 373 pp. 768-774 [ DOI: doi:10.1126/science.abi8976 Pubmed: 34385391 ]
- Tnsc (Protein from Scytonema hofmannii)
- Head-to-head filament of tnsc on double-stranded dna (45 MDa, Complex from Scytonema hofmannii)
ATP-bound TnsC-TniQ complex from ShCAST system
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7n6i
Q-score: 0.299
Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH
Science (2021) 373 pp. 768-774 [ DOI: doi:10.1126/science.abi8976 Pubmed: 34385391 ]
- Helical filament of tnsc monomers bound to dna and tniq (400 kDa, Complex from Scytonema hofmannii)
- Tniq (Protein from Scytonema hofmannii)
- Tnsc (Protein from Scytonema hofmannii)
Focused refined map at the interface of the transcribing Pol II-U1 snRNP complex with 145-nt RNA
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 ]
Focused refined map of U1 snRNP of the transcribing Pol II-U1 snRNP complex with 145-nt RNA
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 ]
Cryo-EM map of the transcribing Pol II-U1 snRNP complex with 155-nt RNA
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 ]
SARS-CoV-2 spike in complex with nanobodies E
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7ksg
Q-score: 0.41
Koenig PA, Das H, Liu H, Kummerer BM, Gohr FN, Jenster LM, Schiffelers LDJ, Tesfamariam YM, Uchima M, Wuerth JD, Gatterdam K, Ruetalo N, Christensen MH, Fandrey CI, Normann S, Todtmann JMP, Pritzl S, Hanke L, Boos J, Yuan M, Zhu X, Schmid-Burgk JL, Kato H, Schindler M, Wilson IA, Geyer M, Ludwig KU, Hallberg BM, Wu NC, Schmidt FI
Science (2021) 371 [ Pubmed: 33436526 DOI: doi:10.1126/science.abe6230 ]
- Nanobody against sars-cov-2 glycoprotein (15 kDa, Protein from Lama glama)
- Complex between sars-cov-2 and a neutralising nanobody e (510 kDa, Complex)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Nanobody e (Complex from Lama glama)