The structure of MPXV polymerase holoenzyme in replicating state
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8hg1
Q-score: 0.486
Peng Q, Xie Y, Kuai L, Wang H, Qi J, Gao GF, Shi Y
Science (2023) 379 pp. 100-105 [ DOI: doi:10.1126/science.ade6360 Pubmed: 36520947 ]
- Dna (25-mer) (7 kDa, DNA from Monkeypox virus)
- Dna polymerase processivity factor component a20 (49 kDa, Protein from Monkeypox virus)
- Dna polymerase (119 kDa, Protein from Monkeypox virus)
- Mpxv dna polymerase holoenzyme (Complex from Monkeypox virus)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna (38-mer) (11 kDa, DNA from Monkeypox virus)
- E4r (25 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 7xm9
Q-score: 0.449
Zhang J, Shi Y, Huang Z, Li Y, Yang B, Gong J, Jiang D
Nat Struct Mol Biol (2022) 29 pp. 1208-1216 [ Pubmed: 36424527 DOI: doi:10.1038/s41594-022-00860-1 ]
- Sodium channel complex (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium channel subunit beta-1,green fluorescent protein (54 kDa, Protein from Aequorea victoria)
- (7~{r})-1'-pentylspiro[6~{h}-furo[3,2-f][1,3]benzodioxole-7,3'-indole]-2'-one (351 Da, Ligand)
- Isoform 3 of sodium channel protein type 9 subunit alpha,green fluorescent protein (255 kDa, Protein from Aequorea victoria)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 7xmf
Q-score: 0.457
Zhang J, Shi Y, Huang Z, Li Y, Yang B, Gong J, Jiang D
Nat Struct Mol Biol (2022) 29 pp. 1208-1216 [ Pubmed: 36424527 DOI: doi:10.1038/s41594-022-00860-1 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium channel subunit beta-1,green fluorescent protein (54 kDa, Protein from Aequorea victoria)
- Sodium channel (Complex from Homo sapiens)
- Isoform 3 of sodium channel protein type 9 subunit alpha,green fluorescent protein (255 kDa, Protein from Aequorea victoria)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- 3-[[4-[3-(4-fluoranyl-2-methyl-phenoxy)azetidin-1-yl]pyrimidin-2-yl]amino]-~{n}-methyl-benzamide (407 Da, Ligand)
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7xmg
Q-score: 0.436
Zhang J, Shi Y, Huang Z, Li Y, Yang B, Gong J, Jiang D
Nat Struct Mol Biol (2022) 29 pp. 1208-1216 [ Pubmed: 36424527 DOI: doi:10.1038/s41594-022-00860-1 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium channel subunit beta-1,green fluorescent protein (54 kDa, Protein from Aequorea victoria)
- Sodium channel (Complex from Homo sapiens)
- Isoform 3 of sodium channel protein type 9 subunit alpha,green fluorescent protein (255 kDa, Protein from Aequorea victoria)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- (1~{z})-~{n}-[2-methyl-3-[(~{e})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{h}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid (516 Da, Ligand)
Cryo-EM structure of POLRMT in free form.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7pzr
Q-score: 0.385
Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hallberg BM, Falkenberg M
Cell (2022) 185 pp. 2309-2323.e24 [ Pubmed: 35662414 DOI: doi:10.1016/j.cell.2022.05.006 ]
- Dna-directed rna polymerase, mitochondrial (137 kDa, Protein from Homo sapiens)
- Polrmt (137 kDa, Complex from Homo sapiens)
Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hallberg BM, Falkenberg M
Cell (2022) 185 pp. 2309-2323.e24 [ Pubmed: 35662414 DOI: doi:10.1016/j.cell.2022.05.006 ]
Yang Y, Shi Y, Schweighauser M, Zhang X, Kotecha A, Murzin AG, Garringer HJ, Cullinane PW, Saito Y, Foroud T, Warner TT, Hasegawa K, Vidal R, Murayama S, Revesz T, Ghetti B, Hasegawa M, Lashley T, Scheres SHW, Goedert M
Nature (2022) 610 pp. 791-795 [ Pubmed: 36108674 DOI: 10.1038/s41586-022-05319-3 ]
Image sets:
The cryo-EM map of the core region from the X. laevis NPC CR subunit
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7fik
Q-score: 0.346
Zhu X, Huang G, Zeng C, Zhan X, Liang K, Xu Q, Zhao Y, Wang P, Wang Q, Zhou Q, Tao Q, Liu M, Lei J, Yan C, Shi Y
Science (2022) 376 pp. eabl8280-eabl8280 [ DOI: doi:10.1126/science.abl8280 Pubmed: 35679404 ]
- Nucleoporin nup88a (82 kDa, Protein from Xenopus laevis)
- Nucleoporin seh1-b (39 kDa, Protein from Xenopus laevis)
- Nup155-prov protein (154 kDa, Protein from Xenopus laevis)
- Nup358 complex, clamps (322 kDa, Protein from Xenopus laevis)
- Nup98 (13 kDa, Protein from Xenopus laevis)
- Mgc154553 protein (41 kDa, Protein from Xenopus laevis)
- Protein sec13 homolog (35 kDa, Protein from Xenopus laevis)
- Xenopus laevis nuclear pore complex (npc) (Complex from Xenopus laevis)
- Nuclear pore complex protein nup133 (111 kDa, Protein from Xenopus laevis)
- Mgc83926 protein (36 kDa, Protein from Xenopus laevis)
- Nuclear pore complex protein nup93 (93 kDa, Protein from Xenopus laevis)
- Outer nup133 (127 kDa, Protein from Xenopus laevis)
- Outer nup160 (162 kDa, Protein from Xenopus laevis)
- Nuclear pore complex protein nup85 (75 kDa, Protein from Xenopus laevis)
- Nuclear pore complex protein nup98-nup96 (191 kDa, Protein from Xenopus laevis)
- Nuclear pore complex protein (105 kDa, Protein from Xenopus laevis)
- Mgc83295 protein (227 kDa, Protein from Xenopus laevis)
CryoEM structure of PS1-containing gamma-secretase in complex with MRK-560
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7y5t
Q-score: 0.56
Guo X, Wang Y, Zhou J, Jin C, Wang J, Jia B, Jing D, Yan C, Lei J, Zhou R, Shi Y
Nat Commun (2022) 13 pp. 6299-6299 [ Pubmed: 36272978 DOI: doi:10.1038/s41467-022-33817-5 ]
- Ps1-containing gamma-secretase in complex with mrk-560 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Nicastrin (78 kDa, Protein from Homo sapiens)
- ~{n}-[4-[2,5-bis(fluoranyl)phenyl]-4-(4-chlorophenyl)sulfonyl-cyclohexyl]-1,1,1-tris(fluoranyl)methanesulfonamide (517 Da, Ligand)
- Gamma-secretase subunit pen-2 (12 kDa, Protein from Homo sapiens)
- Gamma-secretase subunit aph-1a (29 kDa, Protein from Homo sapiens)
- Presenilin-1 (52 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
CryoEM structure of PS2-containing gamma-secretase treated with MRK-560
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7y5x
Q-score: 0.532
Guo X, Wang Y, Zhou J, Jin C, Wang J, Jia B, Jing D, Yan C, Lei J, Zhou R, Shi Y
Nat Commun (2022) 13 pp. 6299-6299 [ Pubmed: 36272978 DOI: doi:10.1038/s41467-022-33817-5 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Nicastrin (78 kDa, Protein from Homo sapiens)
- Presenilin-2 (50 kDa, Protein from Homo sapiens)
- Gamma-secretase subunit pen-2 (12 kDa, Protein from Homo sapiens)
- Gamma-secretase subunit aph-1a (29 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Ps2-containing gamma-secretase complex treated with mrk-560 (Complex from Homo sapiens)