Cryo-EM structure of PGT145 R100aS Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 9d3d
Q-score: 0.474
Mason RD, Zhang B, Morano NC, Shen CH, McKee K, Heimann A, Du R, Nazzari AF, Hodges S, Kanai T, Lin BC, Louder MK, Doria-Rose NA, Zhou T, Shapiro L, Roederer M, Kwong PD, Gorman J
Cell Rep (2025) 44 pp. 115223-115223 [ Pubmed: 39826122 DOI: doi:10.1016/j.celrep.2024.115223 ]
- Phosphate ion (94 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pgt145 r100as heavy chain (26 kDa, Protein from Homo sapiens)
- Bg505 ds-sosip glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Pgt145 r100as fab with hiv-1 bg505 ds-sosip.664 env trimer (Complex from Human immunodeficiency virus 1)
- Hiv-1 bg505 ds-sosip gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Pgt145 light chain (23 kDa, Protein from Homo sapiens)
CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA and puerarin
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 9eqg
Q-score: 0.627
Lyu Q, Xue W, Liu R, Ma Q, Kasaragod VB, Sun S, Li Q, Chen Y, Yuan M, Yang Y, Zhang B, Nie A, Jia S, Shen C, Gao P, Rong W, Yu C, Bi Y, Zhang C, Nan F, Ning G, Rao Z, Yang X, Wang J, Wang W
Nature (2024) 634 pp. 936-943 [ Pubmed: 39261733 DOI: doi:10.1038/s41586-024-07929-5 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Hexane (86 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Water (18 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (56 kDa, Protein from Homo sapiens)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Hexadecane (226 Da, Ligand)
- Decane (142 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Puerarin (416 Da, Ligand)
- Cryoem structure of human full-length alpha1beta3gamma2l gaba(a)r in complex with gaba and puerarin (250 kDa, Complex from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-1 (52 kDa, Protein from Homo sapiens)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8re4
Q-score: 0.47
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ DOI: doi:10.1073/pnas.2309670120 Pubmed: 38170755 ]
- Dna (50-mer) (15 kDa, DNA from Klebsiella oxytoca)
- Zinc ion (65 Da, Ligand)
- Dna (47-mer) (14 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Rna polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex (Complex from Escherichia coli K-12)
- Rna (5'-r(p*gp*cp*cp*gp*c)-3') (1 kDa, RNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (42 kDa, Protein from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8rea
Q-score: 0.427
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ DOI: doi:10.1073/pnas.2309670120 Pubmed: 38170755 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Rna (5'-r(p*gp*cp*cp*gp*c)-3') (1 kDa, RNA from Klebsiella oxytoca)
- Rna polymerase-sigma54 initial transcribing complex - 5nt post-translocated complex (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
- Dna (44-mer) (13 kDa, DNA from Klebsiella oxytoca)
- Rna polymerase sigma-54 factor (42 kDa, Protein from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna (51-mer) (15 kDa, DNA from Klebsiella oxytoca)
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8reb
Q-score: 0.108
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ DOI: doi:10.1073/pnas.2309670120 Pubmed: 38170755 ]
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Dna (43-mer) (13 kDa, DNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Rna polymerase-sigma54 initial transcribing complex - 5nt post-translocated complex (Complex from Escherichia coli K-12)
- Rna (5'-r(p*gp*cp*cp*gp*cp*g)-3') (1 kDa, RNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna (52-mer) (16 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (39 kDa, Protein from Klebsiella oxytoca)
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8rec
Q-score: 0.406
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ DOI: doi:10.1073/pnas.2309670120 Pubmed: 38170755 ]
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*gp*cp*cp*gp*cp*gp*a)-3') (2 kDa, RNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Dna (51-mer) (15 kDa, DNA from Klebsiella oxytoca)
- Rna polymerase sigma-54 factor (39 kDa, Protein from Klebsiella oxytoca)
- Dna (46-mer) (14 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
- Rna polymerase-sigma54 initial transcribing complex - 7nt complex (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 8nt complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8red
Q-score: 0.387
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ DOI: doi:10.1073/pnas.2309670120 Pubmed: 38170755 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Rna polymerase-sigma54 initial transcribing complex - 8nt complex (Complex from Escherichia coli K-12)
- Rna (5'-r(p*gp*cp*cp*gp*cp*gp*ap*u)-3') (2 kDa, RNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Dna (51-mer) (15 kDa, DNA from Klebsiella oxytoca)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
- Dna (46-mer) (14 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (36 kDa, Protein from Klebsiella oxytoca)
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8ree
Q-score: 0.136
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ DOI: doi:10.1073/pnas.2309670120 Pubmed: 38170755 ]
- Zinc ion (65 Da, Ligand)
- Rna polymerase-sigma54 initial transcribing complex - 9nt complex (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Dna (49-mer) (15 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (36 kDa, Protein from Klebsiella oxytoca)
- Rna (5'-r(p*gp*cp*cp*gp*cp*gp*ap*up*c)-3') (2 kDa, RNA from Klebsiella oxytoca)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
- Dna (45-mer) (13 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of human Anion Exchanger 1 bound to Dipyridamole
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8t6u
Q-score: 0.469
Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Zhao Y, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D
Nat Struct Mol Biol (2023) 30 pp. 1495-1504 [ DOI: doi:10.1038/s41594-023-01085-6 Pubmed: 37679563 ]
- Dimeric anion exchanger 1 (slc4a1) (203 kDa, Complex from Homo sapiens)
- Band 3 anion transport protein (58 kDa, Protein from Homo sapiens)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- 2-[[2-[bis(2-hydroxyethyl)amino]-4,8-di(piperidin-1-yl)pyrimido[5,4-d]pyrimidin-6-yl]-(2-hydroxyethyl)amino]ethanol (504 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8t6v
Q-score: 0.479
Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Zhao Y, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D
Nat Struct Mol Biol (2023) 30 pp. 1495-1504 [ DOI: doi:10.1038/s41594-023-01085-6 Pubmed: 37679563 ]
- Dimeric anion exchanger 1 (slc4a1) (203 kDa, Complex from Homo sapiens)
- Band 3 anion transport protein (58 kDa, Protein from Homo sapiens)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (454 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)