BG505.MD39TS Env trimer in complex with Fab from antibody C05
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7sq1
Q-score: 0.406
Xu Z, Walker S, Wise MC, Chokkalingam N, Purwar M, Moore A, Tello-Ruiz E, Wu Y, Majumdar S, Konrath KM, Kulkarni A, Tursi NJ, Zaidi FI, Reuschel EL, Patel I, Obeirne A, Du J, Schultheis K, Gites L, Smith T, Mendoza J, Broderick KE, Humeau L, Pallesen J, Weiner DB, Kulp DW
Nat Commun (2022) 13 pp. 695-695 [ Pubmed: 35121758 DOI: doi:10.1038/s41467-022-28363-z ]
- Transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp160 (52 kDa, Protein from Human immunodeficiency virus 1)
- C05 fab heavy chain (13 kDa, Protein from Mus musculus)
- Bg505.md39ts env trimer in complex with fab from antibody c05 (410 kDa, Complex)
- C05 fab light chain (12 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein 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)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Supplementary proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Nts, rna, ts (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opd
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 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein 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)
- Transcribing pol ii bound to trc factors, spt6 and paf. (Complex)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Supplementary proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Nts, rna, ts (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
Structure of alpha6beta1 integrin in complex with laminin-511
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7cec
Q-score: 0.347
Arimori T, Miyazaki N, Mihara E, Takizawa M, Taniguchi Y, Cabanas C, Sekiguchi K, Takagi J
Nat Commun (2021) 12 pp. 4012-4012 [ Pubmed: 34188035 DOI: doi:10.1038/s41467-021-24184-8 ]
- Laminin subunit beta-1 (8 kDa, Protein from Homo sapiens)
- Laminin subunit alpha-5 (73 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Huts-4 vh(s112c)-sarah,huts-4 vh(s112c)-sarah (19 kDa, Protein from Homo sapiens)
- Integrin beta-1 (50 kDa, Protein from Homo sapiens)
- Ts2/16 vl-sarah(s37c),ts2/16 vl-sarah(s37c) (18 kDa, Protein from Homo sapiens)
- Integrin alpha-6 (69 kDa, Protein from Homo sapiens)
- Quaternary complex of alpha6beta1 integrin, laminin-511, ts2/16 fv-clasp, and huts-4 fv-clasp (286 kDa, Complex from Homo sapiens)
- Laminin subunit gamma-1 (9 kDa, Protein from Homo sapiens)
- Huts-4 vl(c87y)-sarah(s37c),huts-4 vl(c87y)-sarah(s37c) (17 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ts2/16 vh(s112c)-sarah,ts2/16 vh(s112c)-sarah (19 kDa, Protein from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7nwl
Q-score: 0.296
Schumacher S, Dedden D, Nunez RV, Matoba K, Takagi J, Biertumpfel C, Mizuno N
Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abe9716 Pubmed: 33962943 ]
- Manganese (ii) ion (54 Da, Ligand)
- Integrin alpha-5 (110 kDa, Protein from Homo sapiens)
- Ternary complex of integrin a5b1, fibronectin and ts2/16 fv-clasp (210 kDa, Complex from Homo sapiens)
- Ts2/16 vh(s112c)-sarah chimera (19 kDa, Protein from Mus musculus)
- Ts2/16 vl-sarah(s37c) chimera (18 kDa, Protein from Mus musculus)
- Integrin beta-1 (86 kDa, Protein from Homo sapiens)
- Isoform 1 of fibronectin (39 kDa, Protein from Homo sapiens)