Hepatitis B core protein with bound Geraniol
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8pwo
Q-score: 0.597
Khayenko V, Makbul C, Schulte C, Hemmelmann N, Bottcher B, Maric HM
To Be Published
- Capsid protein (21 kDa, Protein from Hepatitis B virus ayw/France/Tiollais/1979)
- Hepatitis b virus (5 MDa, Virus from Hepatitis B virus)
- Geraniol (154 Da, Ligand)
ST171-bound serotonin 5-HT1A receptor - Gi Protein Complex
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8pjk
Q-score: 0.611
Ullrich A, Schneider J, Braz JM, Neu E, Staffen N, Stanek M, Blahova J, Hove T, Albert T, Allikalt A, Lober S, Bhardwaj K, Rodriguez-Rosado S, Fink E, Rasmussen T, Hubner H, Inoue A, Shoichet BK, Basbaum AJ, Bottcher B, Weikert D, Gmeiner P
bioRxiv (2023) [ DOI: doi:10.1101/2023.09.11.557127 ]
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- St171-bound serotonin 5-ht1a receptor - gi protein complex (Complex from Homo sapiens)
- (2r)-1-(heptadecanoyloxy)-3-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (953 Da, Ligand)
- 6-[3-[2-(2-methoxyphenoxy)ethylamino]propoxy]-4~{h}-1,4-benzoxazin-3-one (372 Da, Ligand)
- 5-hydroxytryptamine receptor 1a (51 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
Befiradol-bound serotonin 5-HT1A receptor - Gi Protein Complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8pkm
Q-score: 0.468
Ullrich A, Schneider J, Braz JM, Neu E, Staffen N, Stanek M, Blahova J, Hove T, Albert T, Allikalt A, Lober S, Bhardwaj K, Rodriguez-Rosado S, Fink E, Rasmussen T, Hubner H, Inoue A, Shoichet BK, Basbaum AJ, Bottcher B, Weikert D, Gmeiner P
bioRxiv (2023) [ DOI: doi:10.1101/2023.09.11.557127 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- (2r)-1-(heptadecanoyloxy)-3-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (953 Da, Ligand)
- (3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methylamino]methyl]piperidin-1-yl]methanone (393 Da, Ligand)
- 5-hydroxytryptamine receptor 1a (51 kDa, Protein from Homo sapiens)
- Befiradol-bound serotonin 5-ht1a receptor - gi protein complex (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
70S-PHIKZ014 PHIKZ phage protein occupied ribosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cd1
Q-score: 0.461
Gerovac M, Chihara K, Wicke L, Bottcher B, Lavigne R, Vogel J
Nat Microbiol (2024) 9 pp. 787-800 [ DOI: doi:10.1038/s41564-024-01616-x Pubmed: 38443577 ]
- 70s-phikz014 phikz phage hijacked ribosome (Complex from Pseudomonas aeruginosa PAO1H2O)
- 16s rrna (494 kDa, RNA from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l27 (9 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l21 (11 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l20 (13 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l17 (14 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l32 (6 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l25 (21 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l29 (7 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l18 (12 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l23 (10 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l36 (4 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l30 (6 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s6 (16 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s8 (14 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s12 (13 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s10 (11 kDa, Protein from Pseudomonas aeruginosa PAO1)
- Magnesium ion (24 Da, Ligand)
- 23s rrna (935 kDa, RNA from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s16 (9 kDa, Protein from Pseudomonas aeruginosa PAO1)
- Phikz014 (43 kDa, Protein from Pseudomonas phage phiKZ)
- 5s rrna (38 kDa, RNA from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l4 (21 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s13 (13 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s18 (8 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l35 (7 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s17 (10 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l2 (29 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l31 (7 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s15 (10 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s14 (11 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s7 (17 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l34 (5 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l24 (11 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l15 (15 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l6 (19 kDa, Protein from Pseudomonas aeruginosa PAO1)
- Trna (24 kDa, RNA from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l19 (13 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l13 (16 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s19 (10 kDa, Protein from Pseudomonas aeruginosa PAO1)
- Large ribosomal subunit protein ul22 (11 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s5 (17 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s11 (13 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l16 (15 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s21 (8 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s4 (23 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l28 (9 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s2 (27 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s20 (9 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l9 (15 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l14 (13 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s3 (25 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l3 (22 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 30s ribosomal protein s9 (14 kDa, Protein from Pseudomonas aeruginosa PAO1)
- 50s ribosomal protein l5 (20 kDa, Protein from Pseudomonas aeruginosa PAO1)
cytochrome bd-II type oxidase with bound aurachin D
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ose
Q-score: 0.506
Grauel A, Kagi J, Rasmussen T, Makarchuk I, Oppermann S, Moumbock AFA, Wohlwend D, Muller R, Melin F, Gunther S, Hellwig P, Bottcher B, Friedrich T
Nat Commun (2021) 12 pp. 6498-6498 [ DOI: doi:10.1038/s41467-021-26835-2 Pubmed: 34764272 ]
- Cytochrome bd-ii ubiquinol oxidase subunit 2 (42 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Aurachin d (363 Da, Ligand)
- Heme b/c (618 Da, Ligand)
- Cis-heme d hydroxychlorin gamma-spirolactone (632 Da, Ligand)
- Putative cytochrome bd-ii ubiquinol oxidase subunit appx (3 kDa, Protein from Escherichia coli BW25113)
- Cytochrome bd-ii ubiquinol oxidase subunit 1 (57 kDa, Protein from Escherichia coli BW25113)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bd-ii ubiquinol oxidase (208 kDa, Complex from Escherichia coli BW25113)
Mechanosensitive channel MscS solubilized with LMNG in open conformation
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 7onj
Q-score: 0.637
Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Loffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Bottcher B
PNAS (2021) 118 [ Pubmed: 34376558 DOI: doi:10.1073/pnas.2107095118 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Water (18 Da, Ligand)
- Homoheptameric complex of mscs coordinated with lipids and detergents ddm and lmng (224 kDa, Complex from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Mechanosensitive channel of small conductance (mscs) (31 kDa, Protein from Escherichia coli)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Mechanosensitive channel MscS solubilized with DDM in open conformation
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7oo0
Q-score: 0.559
Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Loffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Bottcher B
PNAS (2021) 118 [ Pubmed: 34376558 DOI: doi:10.1073/pnas.2107095118 ]
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Mechanosensitive channel mscs (31 kDa, Protein from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Homoheptameric complex of mscs coordinated with lipids and detergent ddm (224 kDa, Complex from Escherichia coli)
Mechanosensitive channel MscS solubilized with DDM in closed conformation with added lipid
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7oo6
Q-score: 0.513
Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Loffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Bottcher B
PNAS (2021) 118 [ Pubmed: 34376558 DOI: doi:10.1073/pnas.2107095118 ]
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Homoheptameric complex of mscs coordinated with lipids and detergent ddm (224 kDa, Complex from Escherichia coli)
- Mechanosensitive channel of small conductance (mscs) (31 kDa, Protein from Escherichia coli)
Mechanosensitive channel MscS solubilized with LMNG in open conformation with added lipid
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7ooa
Q-score: 0.622
Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Loffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Bottcher B
PNAS (2021) 118 [ Pubmed: 34376558 DOI: doi:10.1073/pnas.2107095118 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Mechanosensitive channel of small conductance (mscs) (31 kDa, Protein from Escherichia coli SE11)
- Homoheptameric complex of mscs coordinated with lipids and detergents ddm and lmng (224 kDa, Complex from Escherichia coli SE11)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6zyd
Q-score: 0.438
Flegler VJ, Rasmussen A, Rao S, Wu N, Zenobi R, Sansom MSP, Hedrich R, Rasmussen T, Bottcher B
PNAS (2020) 117 pp. 28754-28762 [ Pubmed: 33148804 DOI: doi:10.1073/pnas.2005641117 ]