Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8pg0
Q-score: 0.528
Ciuta AD, Nosol K, Kowal J, Mukherjee S, Ramirez AS, Stieger B, Kossiakoff AA, Locher KP
Nat Commun (2023) 14 pp. 5774-5774 [ DOI: doi:10.1038/s41467-023-41552-8 Pubmed: 37723174 ]
- Bicarbonate ion (61 Da, Ligand)
- Solute carrier organic anion transporter family member 1b3 (77 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Fab19 (light chain, variable region) (23 kDa, Protein from Homo sapiens)
- Human oatp1b3 (180 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab19 (heavy chain, variable region) (25 kDa, Protein from Homo sapiens)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8phw
Q-score: 0.38
Ciuta AD, Nosol K, Kowal J, Mukherjee S, Ramirez AS, Stieger B, Kossiakoff AA, Locher KP
Nat Commun (2023) 14 pp. 5774-5774 [ DOI: doi:10.1038/s41467-023-41552-8 Pubmed: 37723174 ]
- Human oatp1b1 (180 kDa, Complex)
- Solute carrier organic anion transporter family member 1b1 (76 kDa, Protein from Homo sapiens)
- Fab18 (light chain, variable region) (23 kDa, Protein from Homo sapiens)
- Solute carrier organic anion transporter family member 1b1 (Complex from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Fab18 (variable region) (Complex from Homo sapiens)
- Fab18 (heavy chain, variable region) (24 kDa, Protein from Homo sapiens)
- Estrone 3-sulfate (350 Da, Ligand)
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7zlg
Q-score: 0.454
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase cedpy19, in complex with acceptor peptide and bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 7zlh
Q-score: 0.455
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in apo state, bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 7zli
Q-score: 0.496
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in complex with dol25-p-man and bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] [(3~{s},6~{z},10~{e},14~{e})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] hydrogen phosphate (602 Da, Ligand)
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7zlj
Q-score: 0.411
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in ternary complex with dol25-p-c-man and acceptor peptide, bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
- [(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{s},6~{e},10~{z},14~{e})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid (600 Da, Ligand)
ATP-bound AMP-activated protein kinase
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7m74
Q-score: 0.27
Yan Y, Mukherjee S, Harikumar KG, Strutzenberg TS, Zhou XE, Suino-Powell K, Xu TH, Sheldon RD, Lamp J, Brunzelle JS, Radziwon K, Ellis A, Novick SJ, Vega IE, Jones RG, Miller LJ, Xu HE, Griffin PR, Kossiakoff AA, Melcher K
Science (2021) 373 pp. 413-419 [ Pubmed: 34437114 DOI: doi:10.1126/science.abe7565 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine (399 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Fab heavy chain (24 kDa, Protein from Homo sapiens)
- 5'-amp-activated protein kinase catalytic subunit alpha-1 (56 kDa, Protein from Homo sapiens)
- Mbp-fused atp bound ampk in complex with c-compound stabilized by fab and a nanobody (Complex from Homo sapiens)
- 5'-amp-activated protein kinase subunit beta-2 (22 kDa, Protein from Homo sapiens)
- 5'-amp-activated protein kinase subunit gamma-1 (34 kDa, Protein from Homo sapiens)
- Fab light chain (22 kDa, Protein from Homo sapiens)
- Nanobody (13 kDa, Protein from Lama glama)
- Maltose/maltodextrin abc transporter substrate-binding protein male (40 kDa, Protein from Escherichia coli)
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 7jhg
Q-score: 0.345
Yan Y, Mukherjee S, Harikumar KG, Strutzenberg TS, Zhou XE, Suino-Powell K, Xu TH, Sheldon RD, Lamp J, Brunzelle JS, Radziwon K, Ellis A, Novick SJ, Vega IE, Jones RG, Miller LJ, Xu HE, Griffin PR, Kossiakoff AA, Melcher K
Science (2021) 373 pp. 413-419 [ Pubmed: 34437114 DOI: doi:10.1126/science.abe7565 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- Nanobody (17 kDa, Protein from synthetic construct)
- 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine (399 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 5'-amp-activated protein kinase catalytic subunit alpha-1 (56 kDa, Protein from Homo sapiens)
- Cryo-em structure of atp-bound fully inactive ampk in complex with dorsomorphin (compound c) and fab-nanobody (220 kDa, Complex)
- Fab light chain (23 kDa, Protein from synthetic construct)
- 5'-amp-activated protein kinase subunit gamma-1 (34 kDa, Protein from Homo sapiens)
- 5'-amp-activated protein kinase subunit beta-2 (22 kDa, Protein from Homo sapiens)
- Fab-nanobody (Complex from synthetic construct)
- Fab heavy chain (25 kDa, Protein from synthetic construct)
- Maltodextrin-binding protein (40 kDa, Protein from Escherichia coli K-12)
- Atp-bound fully inactive ampk in complex with dorsomorphin (compound c) (Complex from Homo sapiens)
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody
Resolution: 3.92 Å
EM Method: Single-particle
Fitted PDBs: 7jhh
Q-score: 0.279
Yan Y, Mukherjee S, Harikumar KG, Strutzenberg TS, Zhou XE, Suino-Powell K, Xu TH, Sheldon RD, Lamp J, Brunzelle JS, Radziwon K, Ellis A, Novick SJ, Vega IE, Jones RG, Miller LJ, Xu HE, Griffin PR, Kossiakoff AA, Melcher K
Science (2021) 373 pp. 413-419 [ Pubmed: 34437114 DOI: doi:10.1126/science.abe7565 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- Nanobody (17 kDa, Protein from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 5'-amp-activated protein kinase catalytic subunit alpha-1 (56 kDa, Protein from Homo sapiens)
- Fab light chain (23 kDa, Protein from synthetic construct)
- 5'-amp-activated protein kinase subunit beta-2 (22 kDa, Protein from Homo sapiens)
- Ampk complex with fab and nanobody (220 kDa, Complex)
- 5'-amp-activated protein kinase subunit gamma-1 (34 kDa, Protein from Homo sapiens)
- Fab, nanobody (Complex from synthetic construct)
- Fab heavy chain (25 kDa, Protein from synthetic construct)
- Ampk (Complex from Homo sapiens)
- Maltodextrin-binding protein (40 kDa, Protein from Escherichia coli K-12)