Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ovc
Q-score: 0.598
Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI
Nat Commun (2024) 15 pp. 5276-5276 [ Pubmed: 38902248 DOI: doi:10.1038/s41467-024-49628-9 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (869 Da, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Heme c (618 Da, Ligand)
- Water (18 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (2 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8ti1
Q-score: 0.419
Driggers CM, Kuo YY, Zhu P, ElSheikh A, Shyng SL
Nat Commun (2024) 15 pp. 2502-2502 [ Pubmed: 38509107 DOI: doi:10.1038/s41467-024-46751-5 ]
- Water (18 Da, Ligand)
- Kir6.2-q52r/sur1 open channel (880 kDa, Complex from Rattus norvegicus)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- [(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)
- Sur1 (177 kDa, Protein from Mesocricetus auratus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Atp-sensitive inward rectifier potassium channel 11 (43 kDa, Protein from Rattus norvegicus)
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8ti2
Q-score: 0.394
Driggers CM, Kuo YY, Zhu P, ElSheikh A, Shyng SL
Nat Commun (2024) 15 pp. 2502-2502 [ Pubmed: 38509107 DOI: doi:10.1038/s41467-024-46751-5 ]
- Water (18 Da, Ligand)
- Kir6.2-q52r/sur1 open channel (880 kDa, Complex from Rattus norvegicus)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- [(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)
- Sur1 (177 kDa, Protein from Mesocricetus auratus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Atp-sensitive inward rectifier potassium channel 11 (43 kDa, Protein from Rattus norvegicus)
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 ]
- Glycine receptor subunit alphaz1 (52 kDa, Protein from Danio rerio)
- Strychnine (334 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 receptor beta subunit 2 (65 kDa, Protein from Danio rerio)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- [(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)
T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a8c
Q-score: 0.549
van den Berg B, Silale A, Basle A, Brandner AF, Mader SL, Khalid S
PNAS (2022) 119 pp. e2211672119-e2211672119 [ DOI: doi:10.1073/pnas.2211672119 Pubmed: 36215462 ]
- [(2r,3s,4r,5r,6r)-2-[[(2r,4r,5r,6r)-6-[(1r)-1,2-bis(oxidanyl)ethyl]-4-[(2r,4r,5r,6r)-6-[(1r)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3r)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2r,3s,4r,5r,6r)-3-oxidanyl-4-[(3s)-3-oxidanyltetradecanoyl]oxy-5-[[(3r)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate (1 kDa, Ligand)
- T5 phage receptor-binding protein pb5 bound to ferrichrome transporter fhua (148 kDa, Complex from Escherichia phage T5)
- Ferrichrome outer membrane transporter/phage receptor (78 kDa, Protein from Escherichia coli K-12)
- Receptor-binding protein pb5 (69 kDa, Protein from Escherichia phage T5)
CryoEM structure of SERINC from Drosophila melanogaster
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 6sp2
Q-score: 0.482
Pye VE, Rosa A, Bertelli C, Struwe WB, Maslen SL, Corey R, Liko I, Hassall M, Mattiuzzo G, Ballandras-Colas A, Nans A, Takeuchi Y, Stansfeld PJ, Skehel JM, Robinson CV, Pizzato M, Cherepanov P
Nat Struct Mol Biol (2020) 27 pp. 78-83 [ DOI: doi:10.1038/s41594-019-0357-0 Pubmed: 31907454 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Serinc homo-hexamer (328 kDa, Complex from Drosophila melanogaster)
- Membrane protein tms1d (54 kDa, Protein from Drosophila melanogaster)