Single particle reconstruction of the human LINE-1 ORF2p without substrate (apo)
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
Structure of LINE-1 ORF2p with template:primer hybrid
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8sxt
Q-score: 0.339
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
- Rna template (5 kDa, RNA from synthetic construct)
- Dna primer (3 kDa, DNA from synthetic construct)
Structure of LINE-1 ORF2p with an oligo(A) template
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8sxu
Q-score: 0.185
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Rna (25-mer) (8 kDa, RNA from synthetic construct)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 7uhy
Q-score: 0.415
Valenstein ML, Rogala KB, Lalgudi PV, Brignole EJ, Gu X, Saxton RA, Chantranupong L, Kolibius J, Quast JP, Sabatini DM
Nature (2022) 607 pp. 610-616 [ DOI: doi:10.1038/s41586-022-04939-z Pubmed: 35831510 ]
- Isoform b of nucleoporin seh1 (46 kDa, Protein from Homo sapiens)
- Protein sec13 homolog (35 kDa, Protein from Homo sapiens)
- Gator complex protein mios (100 kDa, Protein from Homo sapiens)
- Unknown (698 Da, Protein from Homo sapiens)
- Gator complex protein wdr24 (88 kDa, Protein from Homo sapiens)
- Gator complex protein wdr59 (109 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Unknown (1 kDa, Protein from Homo sapiens)
- Human gator2 (1 MDa, Complex from Homo sapiens)
Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 6ulg
Q-score: 0.467
Shen K, Rogala KB, Chou HT, Huang RK, Yu Z, Sabatini DM
Cell (2019) 179 pp. 1319-1329.e8 [ Pubmed: 31704029 DOI: doi:10.1016/j.cell.2019.10.036 ]
- Folliculin (64 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor5 (9 kDa, Protein from Homo sapiens)
- Ras-related gtp-binding protein a (36 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor2 (13 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor1 (17 kDa, Protein from Homo sapiens)
- Ras-related gtp-binding protein c (44 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Nonameric complex of flcn-fnip2 with its substrate rag gtpases and the scaffolding protein complex ragulator (380 kDa, Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Ragulator complex protein lamtor4 (10 kDa, Protein from Homo sapiens)
- Folliculin-interacting protein 2 (122 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor3 (13 kDa, Protein from Homo sapiens)
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 6u62
Q-score: 0.513
Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM
Science (2019) 366 pp. 468-475 [ Pubmed: 31601708 DOI: doi:10.1126/science.aay0166 ]
- Ras-related gtp-binding protein c (44 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Ragulator complex protein lamtor4 (10 kDa, Protein from Homo sapiens)
- Regulatory-associated protein of mtor (154 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor2 (13 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor3 (17 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor5 (9 kDa, Protein from Homo sapiens)
- Raptor-rag-ragulator (Complex from Homo sapiens)
- Ras-related gtp-binding protein a (36 kDa, Protein from Homo sapiens)
- Ragulator complex protein lamtor1 (17 kDa, Protein from Homo sapiens)
Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM
Science (2019) 366 pp. 468-475 [ DOI: doi:10.1126/science.aay0166 Pubmed: 31601708 ]
cryo-EM structure of mTORC1 bound to PRAS40-fused active RagA/C GTPases
Resolution: 5.5 Å
EM Method: Single-particle
Fitted PDBs: 6sb0
Q-score: 0.237
Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL
Science (2019) 366 pp. 203-210 [ Pubmed: 31601764 DOI: doi:10.1126/science.aax3939 ]
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Raga/c (Complex from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Ras-related gtp-binding protein c (44 kDa, Protein from Homo sapiens)
- Proline-rich akt1 substrate 1 (27 kDa, Protein from Homo sapiens)
- Ras-related gtp-binding protein a (36 kDa, Protein from Homo sapiens)
- Mtor,serine/threonine-protein kinase mtor,mtor,serine/threonine-protein kinase mtor (287 kDa, Protein from Homo sapiens)
- Mtorc1 (Complex from Homo sapiens)
- Regulatory-associated protein of mtor (149 kDa, Protein from Homo sapiens)
- Cryoem structure of mtorc1 bound to raga/c complex (1 MDa, Complex)
- Target of rapamycin complex subunit lst8 (35 kDa, Protein from Homo sapiens)
cryo-EM structure of mTORC1 bound to active RagA/C GTPases
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 6sb2
Q-score: 0.211
Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL
Science (2019) 366 pp. 203-210 [ Pubmed: 31601764 DOI: doi:10.1126/science.aax3939 ]
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Raga/c (Complex from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cryo-em structure of mtorc1 bound to active raga/c complex (1 MDa, Complex)
- Ras-related gtp-binding protein c (44 kDa, Protein from Homo sapiens)
- Ras-related gtp-binding protein a (36 kDa, Protein from Homo sapiens)
- Mtorc1 (Complex from Homo sapiens)
- Regulatory-associated protein of mtor (149 kDa, Protein from Homo sapiens)
- Mtor,serine/threonine-protein kinase mtor,mtor,serine/threonine-protein kinase mtor (287 kDa, Protein from Homo sapiens)
- Target of rapamycin complex subunit lst8 (35 kDa, Protein from Homo sapiens)