TRPM7 structure in complex with anticancer agent CCT128930 in closed state
Resolution: 2.45 Å
EM Method: Single-particle
Fitted PDBs: 8w2l
Q-score: 0.539
Nadezhdin KD, Correia L, Shalygin A, Aktolun M, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Cell Rep (2024) 43 pp. 114108-114108 [ Pubmed: 38615321 DOI: doi:10.1016/j.celrep.2024.114108 ]
- Calcium ion (40 Da, Ligand)
- Green fluorescent protein,transient receptor potential cation channel subfamily m member 7 (175 kDa, Protein from Mus musculus)
- 4-(4-chlorobenzyl)-1-(7h-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium (342 Da, Ligand)
- Complex of trpm7 with antagonist cct128930 (700 kDa, Complex)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in apo state
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 8si2
Q-score: 0.523
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- Sample 1 (700 kDa, Complex from Mus musculus)
- Sodium ion (22 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of TRPM7 in GDN detergent in apo state
Resolution: 2.61 Å
EM Method: Single-particle
Fitted PDBs: 8si3
Q-score: 0.491
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- Calcium ion (40 Da, Ligand)
- Sample 1 (700 kDa, Complex from Mus musculus)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of TRPM7 N1098Q mutant in GDN detergent in open state
Resolution: 2.46 Å
EM Method: Single-particle
Fitted PDBs: 8si4
Q-score: 0.462
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- Calcium ion (40 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- Sample 1 (700 kDa, Complex from Mus musculus)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in complex with agonist naltriben in open state
Resolution: 2.17 Å
EM Method: Single-particle
Fitted PDBs: 8si5
Q-score: 0.566
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- Calcium ion (40 Da, Ligand)
- Sample 1 (700 kDa, Complex from Mus musculus)
- (4bs,8r,8as,14br)-7-(cyclopropylmethyl)-5,6,7,8,9,14b-hexahydro-8ah-4,8-methanobis[1]benzofuro[3,2-e:2',3'-g]isoquinoline-1,8a-diol (415 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in complex with agonist naltriben in closed state
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 8si6
Q-score: 0.24
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- Calcium ion (40 Da, Ligand)
- Sample 1 (700 kDa, Complex from Mus musculus)
- (4bs,8r,8as,14br)-7-(cyclopropylmethyl)-5,6,7,8,9,14b-hexahydro-8ah-4,8-methanobis[1]benzofuro[3,2-e:2',3'-g]isoquinoline-1,8a-diol (415 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of TRPM7 in GDN detergent in complex with inhibitor VER155008 in closed state
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 8si7
Q-score: 0.446
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- 4-[[(2r,3s,4r,5r)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile (556 Da, Ligand)
- Sample 1 (700 kDa, Complex from Mus musculus)
- Calcium ion (40 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Water (18 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8si8
Q-score: 0.443
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- 4-[[(2r,3s,4r,5r)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile (556 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- Sample 1 (700 kDa, Complex from Mus musculus)
- Calcium ion (40 Da, Ligand)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8sia
Q-score: 0.422
Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI
Nat Commun (2023) 14 pp. 2639-2639 [ DOI: doi:10.1038/s41467-023-38362-3 Pubmed: 37156763 ]
- Calcium ion (40 Da, Ligand)
- Transient receptor potential cation channel subfamily m member 7 (146 kDa, Protein from Mus musculus)
- Sample 1 (700 kDa, Complex from Mus musculus)
- N-[(1r)-1,2,3,4-tetrahydronaphthalen-1-yl]-1h-benzimidazol-2-amine (263 Da, Ligand)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)