2.02 angstrom cryo-EM structure of the pump-like channelrhodopsin ChRmine
Resolution: 2.02 Å
EM Method: Single-particle
Fitted PDBs: 7w9w
Q-score: 0.708
Kishi KE, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang PY, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K, Kato HE
Cell (2022) 185 pp. 672- [ DOI: doi:10.1016/j.cell.2022.01.007 Pubmed: 35114111 ]
- Water (18 Da, Ligand)
- Chrmine (Complex from Rhodomonas lens)
- Retinal (284 Da, Ligand)
- Chrmine (35 kDa, Protein from Rhodomonas lens)
- Cholesterol (386 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
2.12 angstrom cryo-EM map of the pump-like channelrhodopsin ChRmine with Fab antibody fragment
Kishi KE, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang PY, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K, Kato HE
Cell (2022) 185 pp. 672-689.e23 [ Pubmed: 35114111 DOI: doi:10.1016/j.cell.2022.01.007 ]
- Chrmine with fab (Protein from Rhodomonas lens)
- Chrmine (Complex from Rhodomonas lens)
Cryo-EM structure of a class A orphan GPCR in complex with Gi
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7vug
Q-score: 0.445
Zhou Y, Daver H, Trapkov B, Wu L, Wu M, Harpsoe K, Gentry PR, Liu K, Larionova M, Liu J, Chen N, Brauner-Osborne H, Gloriam DE, Hua T, Liu ZJ
Cell Res (2022) 32 pp. 210-213 [ DOI: doi:10.1038/s41422-021-00591-w Pubmed: 34916631 ]
- 3-chloranyl-n-[2-oxidanylidene-2-[[(1s)-1-phenylethyl]amino]ethyl]benzamide (316 Da, Ligand)
- Ternary complex of ligand, gpcr and g protein (180 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bacillus circulans)
- Endo-1,4-beta-xylanase,probable g-protein coupled receptor 139 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- 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)
- Chimera of endo-1,4-beta-xylanase and probable g-protein coupled receptor 139 (60 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Scfv16 (Complex)
- Scfv16 (27 kDa, Protein from Homo sapiens)
Cryo-EM structure of a class A orphan GPCR
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 7vuh
Q-score: 0.409
Zhou Y, Daver H, Trapkov B, Wu L, Wu M, Harpsoe K, Gentry PR, Liu K, Larionova M, Liu J, Chen N, Brauner-Osborne H, Gloriam DE, Hua T, Liu ZJ
Cell Res (2022) 32 pp. 210-213 [ DOI: doi:10.1038/s41422-021-00591-w Pubmed: 34916631 ]
- Isoform gnas-2 of guanine nucleotide-binding protein g(s) subunit alpha isoforms short (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- 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)/g(s)/g(o) subunit gamma-2 (Complex from Homo sapiens)
- Nanobody 35 (Complex from Bacillus circulans)
- Chimera of endo-1,4-beta-xylanase and probable g-protein coupled receptor 139 (60 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Homo sapiens)
- 3-chloranyl-n-[2-oxidanylidene-2-[[(1s)-1-phenylethyl]amino]ethyl]benzamide (316 Da, Ligand)
- Nanobody 35 (17 kDa, Protein from Homo sapiens)
- Endo-1,4-beta-xylanase,probable g-protein coupled receptor 139 (Complex)
- Isoform gnas-2 of guanine nucleotide-binding protein g(s) subunit alpha isoforms short (30 kDa, Protein from Homo sapiens)
- Ternary complex of ligand, gpcr and g protein (150 kDa, Complex from Homo sapiens)
Structure of a membrane protein
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6lbh
Q-score: 0.461
Jin F, Sun M, Fujii T, Yamada Y, Wang J, Maturana AD, Wada M, Su S, Ma J, Takeda H, Kusakizako T, Tomita A, Nakada-Nakura Y, Liu K, Uemura T, Nomura Y, Nomura N, Ito K, Nureki O, Namba K, Iwata S, Yu Y, Hattori M
PLoS Biol (2021) 19 pp. e3001231-e3001231 [ Pubmed: 33905418 DOI: doi:10.1371/journal.pbio.3001231 ]
- Fab light chain (23 kDa, Protein from Mus musculus)
- Mgte-fab complex (Complex from Thermus thermophilus)
- Fab heavy chain (24 kDa, Protein from Mus musculus)
- Magnesium transporter mgte (19 kDa, Protein from Thermus thermophilus HB8)
Cryo-EM structure of a class A GPCR
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6lfm
Q-score: 0.461
Liu K, Wu L, Yuan S, Wu M, Xu Y, Sun Q, Li S, Zhao S, Hua T, Liu ZJ
Nature (2020) 585 pp. 135-140 [ Pubmed: 32610344 DOI: doi:10.1038/s41586-020-2492-5 ]
- Cholesterol (386 Da, Ligand)
- Interleukin-8 (8 kDa, Protein from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- 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)
- Ternary complex of chemokine, gpcr and g protein (150 kDa, Complex from Homo sapiens)
- C-x-c chemokine receptor type 2 (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of a class A GPCR monomer
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6lfo
Q-score: 0.441
Liu K, Wu L, Yuan S, Wu M, Xu Y, Sun Q, Li S, Zhao S, Hua T, Liu ZJ
Nature (2020) 585 pp. 135-140 [ DOI: doi:10.1038/s41586-020-2492-5 Pubmed: 32610344 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Interleukin-8 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- C-x-c chemokine receptor type 2 (40 kDa, Protein from Homo sapiens)
- Ternary complex of chemokine-monomer, gpcr and g protein (150 kDa, Complex from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
Umeda R, Satouh Y, Takemoto M, Nakada-Nakura Y, Liu K, Yokoyama T, Shirouzu M, Iwata S, Nomura N, Sato K, Ikawa M, Nishizawa T, Nureki O
Nat Commun (2020) 11 pp. 1606-1606 [ Pubmed: 32231207 DOI: doi:10.1038/s41467-020-15459-7 ]
the CD9 and EWI-2 complex attached to an anti-CD9 Fab fragment
Umeda R, Satouh Y, Takemoto M, Nakada-Nakura Y, Liu K, Yokoyama T, Shirouzu M, Iwata S, Nomura N, Sato K, Ikawa M, Nishizawa T, Nureki O
Nat Commun (2020) 11 pp. 1606-1606 [ Pubmed: 32231207 DOI: doi:10.1038/s41467-020-15459-7 ]
Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, Gu Y, Jafari AJ, Louder MK, O'Dell S, Rowshan AP, Viox EG, Wang Y, Choi CW, Corcoran MM, Corrigan AR, Dandey VP, Eng ET, Geng H, Foulds KE, Guo Y, Kwon YD, Lin B, Liu K, Mason RD, Nason MC, Ohr TY, Ou L, Rawi R, Sarfo EK, Schon A, Todd JP, Wang S, Wei H, Wu W, Mullikin JC, Bailer RT, Doria-Rose NA, Karlsson Hedestam GB, Scorpio DG, Overbaugh J, Bloom JD, Carragher B, Potter CS, Shapiro L, Kwong PD, Mascola JR
Cell (2019) 178 pp. 567-584.e19 [ Pubmed: 31348886 DOI: doi:10.1016/j.cell.2019.06.030 ]
- A12v163-b.01 heavy chain (Protein from Macaca mulatta)
- Pgt122 heavy chain (Protein from Homo sapiens)
- Hiv-1 env bg505 ds-sosip gp41 (Protein from Human immunodeficiency virus 1)
- Quaternary complex of hiv-1 env bg505 ds-sosip with antibodies a12v163-b.01, vrc03 and pgt122. (630 kDa, Complex)
- Pgt122 (Complex from Homo sapiens)
- A12v163-b.01 light chain (Protein from Macaca mulatta)
- Hiv-1 env bg505 ds-sosip gp41 (Complex from Human immunodeficiency virus 1)
- Hiv-1 env bg505 ds-sosip gp120 (Protein from Human immunodeficiency virus 1)
- Vrc03 (Complex from Homo sapiens)
- A12v163-b.01 (Complex from Macaca mulatta)
- Pgt122 light chain (Protein from Homo sapiens)
- Vrc03 light chain (Protein from Homo sapiens)
- Hiv-1 env bg505 ds-sosip gp120 (Complex from Human immunodeficiency virus 1)
- Vrc03 heavy chain (Protein from Homo sapiens)