Cryo-EM structure of the mammalian peptide transporter PepT2 bound to cloxacillin, pose 1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9bit
Q-score: 0.539
Parker JL, Deme JC, Lichtinger SM, Kuteyi G, Biggin PC, Lea SM, Newstead S
Nat Commun (2024) 15 pp. 8755-8755 [ DOI: doi:10.1038/s41467-024-53096-6 Pubmed: 39384780 ]
- Complex of the mammalian peptide transporter pept2 with nanobody and bound cloxacillin, pose 1 (Complex from Rattus norvegicus)
- Nanobody (Complex from Lama glama)
- Cloxacillin (435 Da, Ligand)
- Pept2 (Complex from Rattus norvegicus)
- Nanobody (14 kDa, Protein from Lama glama)
- Solute carrier family 15 member 2 (82 kDa, Protein from Rattus norvegicus)
Cryo-EM structure of the mammalian peptide transporter PepT2 bound to cloxacillin, pose 2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9biu
Q-score: 0.548
Parker JL, Deme JC, Lichtinger SM, Kuteyi G, Biggin PC, Lea SM, Newstead S
Nat Commun (2024) 15 pp. 8755-8755 [ DOI: doi:10.1038/s41467-024-53096-6 Pubmed: 39384780 ]
- Nanobody (Complex from Lama glama)
- Cloxacillin (435 Da, Ligand)
- Pept2 (Complex from Rattus norvegicus)
- Nanobody (14 kDa, Protein from Lama glama)
- Solute carrier family 15 member 2 (82 kDa, Protein from Rattus norvegicus)
- Complex of the mammalian peptide transporter pept2 with nanobody and bound cloxacillin, pose 2 (Complex from Rattus norvegicus)
Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 5.5
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8i47
Q-score: 0.519
Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S
Nat Commun (2024) 15 pp. 2967-2967 [ DOI: doi:10.1038/s41467-024-47370-w Pubmed: 38580666 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Proton-gated ion channel (35 kDa, Protein from Gloeobacter violaceus)
- Water (18 Da, Ligand)
- Pentameric ligand-gated ion channel (Complex from Gloeobacter violaceus)
Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in closed state
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8i48
Q-score: 0.547
Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S
Nat Commun (2024) 15 pp. 2967-2967 [ DOI: doi:10.1038/s41467-024-47370-w Pubmed: 38580666 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Pentameric ligand-gated ion channel (Complex from Gloeobacter violaceus)
- Proton-gated ion channel (35 kDa, Protein from Gloeobacter violaceus)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 2.5
Resolution: 2.6476 Å
EM Method: Single-particle
Fitted PDBs: 8jj3
Q-score: 0.624
Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S
Nat Commun (2024) 15 pp. 2967-2967 [ DOI: doi:10.1038/s41467-024-47370-w Pubmed: 38580666 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Pentameric ligand-gated ion channel (Complex from Gloeobacter violaceus)
- Proton-gated ion channel (35 kDa, Protein from Gloeobacter violaceus)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in open state
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8wcr
Q-score: 0.625
Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S
Nat Commun (2024) 15 pp. 2967-2967 [ DOI: doi:10.1038/s41467-024-47370-w Pubmed: 38580666 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Pentameric ligand-gated ion channel (Complex from Gloeobacter violaceus)
- Proton-gated ion channel (35 kDa, Protein from Gloeobacter violaceus)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7tu9
Q-score: 0.521
Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S
Nat Commun (2023) 14 pp. 1363- [ DOI: doi:10.1038/s41467-023-37106-7 ]
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Strychnine (334 Da, Ligand)
- Glycine receptor beta subunit 2 (65 kDa, Protein from Danio rerio)
- Glycine receptor subunit alphaz1 (52 kDa, Protein from Danio rerio)
- 1,2-dimyristoyl-sn-glycero-3-phosphocholine (678 Da, Ligand)
- Zebrafish alpha1 betab heteromeric glycine receptor (250 kDa, Complex from Danio rerio)
Alpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7tvi
Q-score: 0.375
Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S
Nat Commun (2023) 14 pp. 1363- [ DOI: doi:10.1038/s41467-023-37106-7 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glycine receptor beta subunit 2 (65 kDa, Protein from Danio rerio)
- Glycine receptor subunit alphaz1 (52 kDa, Protein from Danio rerio)
- Zebrafish alpha1 betab heteromeric glycine receptor (250 kDa, Complex from Danio rerio)
- Glycine (75 Da, Ligand)
Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM Ivermectin State
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8fe1
Q-score: 0.527
Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S
Nat Commun (2023) 14 pp. 1363-1363 [ DOI: doi:10.1038/s41467-023-37106-7 Pubmed: 36914669 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- (2ae,4e,5's,6s,6'r,7s,8e,11r,13r,15s,17ar,20r,20ar,20bs)-6'-[(2s)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2h,7h-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-o-(2,6-dideoxy-3-o-methyl-alpha-l-arabino-hexopyranosyl)-3-o-methyl-alpha-l-arabino-hexopyranoside (875 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Glycine receptor beta subunit 2 (65 kDa, Protein from Danio rerio)
- Glycine receptor subunit alphaz1 (52 kDa, Protein from Danio rerio)
- Decane (142 Da, Ligand)
- Zebrafish alpha1 betab heteromeric glycine receptor (250 kDa, Complex from Danio rerio)
- 1,2-dimyristoyl-sn-glycero-3-phosphocholine (678 Da, Ligand)
- Glycine (75 Da, Ligand)
Full length alpha1 Glycine receptor in presence of 32uM Tetrahydrocannabinol
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7m6m
Q-score: 0.46
Kumar A, Kindig K, Rao S, Zaki AM, Basak S, Sansom MSP, Biggin PC, Chakrapani S
Nat Commun (2022) 13 pp. 4862-4862 [ Pubmed: 35982060 DOI: doi:10.1038/s41467-022-32594-5 ]
- Glycine receptor subunit alpha z1 (250 MDa, Complex from Danio rerio)
- (6ar,10ar)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6h-benzo[c]chromen-1-ol (314 Da, Ligand)
- Glycine receptor subunit alphaz1 (50 kDa, Protein from Danio rerio)