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)
Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
Resolution: 1.67 Å
EM Method: Single-particle
Fitted PDBs: 8a3d
Q-score: 0.769
Faille A, Dent KC, Pellegrino S, Jaako P, Warren AJ
bioRxiv (2023) [ Pubmed: 36909531 DOI: doi:10.1101/2023.02.28.530191 ]
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- (3beta)-o~3~-[(2r)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine (545 Da, Ligand)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (11 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Homo sapiens)
- Human mature large subunit of the ribosome with eif6 bound (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 5s ribosomal rna (38 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- Ribosomal protein ul29 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- 5.8s ribosomal rna (50 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (238 Da, Ligand)
- 28s ribosomal rna (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7qrm
Q-score: 0.617
Sarewicz M, Szwalec M, Pintscher S, Indyka P, Rawski M, Pietras R, Mielecki B, Koziej L, Jaciuk M, Glatt S, Osyczka A
Sci Adv (2023) 9 pp. eadd9688-eadd9688 [ Pubmed: 36638176 DOI: doi:10.1126/sciadv.add9688 ]
- Cytochrome b6-f complex subunit 7 (3 kDa, Protein from spinach)
- Cytochrome b6-f complex subunit 6 (3 kDa, Protein from spinach)
- Cytochrome b6-f complex subunit 5 (4 kDa, Protein from spinach)
- Chlorophyll a (893 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome f (35 kDa, Protein from spinach)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- Cytochrome b6-f complex subunit 8 (3 kDa, Protein from spinach)
- Cytochrome b6-f complex subunit 4 (17 kDa, Protein from spinach)
- Cytochrome b6 (24 kDa, Protein from spinach)
- Undecyl-maltoside (496 Da, Ligand)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Heme c (618 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Cytochrome b6-f complex iron-sulfur subunit, chloroplastic (24 kDa, Protein from spinach)
- Cytochrome b6f complex (220 kDa, Complex from Spinacia oleracea)
The open state mouse TRPM8 structure in complex with the cooling agonist C3, AITC, and PI(4,5)P2
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8e4l
Q-score: 0.407
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
- [(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)
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- Nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane (260 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- 3-isothiocyanatoprop-1-ene (99 Da, Ligand)
The intermediate C2-state mouse TRPM8 structure in complex with the cooling agonist C3 and PI(4,5)P2
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8e4m
Q-score: 0.384
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- Nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane (260 Da, Ligand)
- Calcium ion (40 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)
The closed C1-state mouse TRPM8 structure in complex with PI(4,5)P2
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8e4n
Q-score: 0.436
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- [(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)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
The closed C1-state mouse TRPM8 structure in complex with putative PI(4,5)P2
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8e4o
Q-score: 0.425
Yin Y, Zhang F, Feng S, Butay KJ, Borgnia MJ, Im W, Lee SY
Science (2022) 378 pp. eadd1268-eadd1268 [ DOI: doi:10.1126/science.add1268 Pubmed: 36227998 ]
- Transient receptor potential cation channel subfamily m member 8 (Complex from Mus musculus)
- [(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)
- Transient receptor potential cation channel subfamily m member 8 (131 kDa, Protein from Mus musculus)
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)
Phophorylated Drs2p-Cdc50p in a PS and ATP-bound E2P state
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7pem
Q-score: 0.516
Wang Y, Lyons JA, Timcenko M, Kummerer F, de Groot BL, Nissen P, Gapsys V, Lindorff-Larsen K
To Be Published
- Binary complex of drs2p-cdc50p with the regulatory lipid pi4p and transport substrate ps (180 kDa, Complex from Saccharomyces cerevisiae)
- Cell division control protein 50 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Probable phospholipid-transporting atpase drs2 (154 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- O-[(r)-[(2s)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-d-serine (764 Da, Ligand)
- (2r)-1-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (967 Da, Ligand)
- Water (18 Da, Ligand)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7xve
Q-score: 0.526
Huang G, Wu Q, Li Z, Jin X, Huang X, Wu T, Pan X, Yan N
PNAS (2022) 119 pp. e2209164119-e2209164119 [ Pubmed: 35878056 DOI: doi:10.1073/pnas.2209164119 ]
- Sodium channel protein type 9 subunit alpha (230 kDa, Protein from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- (2s,3r,4e)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate (421 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Ternary complex of alpha1/beta1/beta2 (300 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)