Cryo-EM structure of Light-harvesting complex from Spinacia oleracea
Resolution: 2.17 Å
EM Method: Single-particle
Fitted PDBs: 8y15
Q-score: 0.709
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ Pubmed: 39346626 DOI: doi:10.1093/pnasnexus/pgae405 ]
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- Light-harvesting complex ii from spinacia oleracea (700 kDa, Complex from Spinacia oleracea)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lutein (568 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
Cryo-EM structure of in vitro reconstituted Light-harvesting complex II trimer
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8yee
Q-score: 0.678
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ Pubmed: 39346626 DOI: doi:10.1093/pnasnexus/pgae405 ]
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Spinacia oleracea)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- In vitro reconstituted light-harvesting complex ii (120 kDa, Complex from Spinacia oleracea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lutein (568 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
Cryo-EM structure of light-harvesting complex II with C1 symmetry
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ Pubmed: 39346626 DOI: doi:10.1093/pnasnexus/pgae405 ]
- Light-harvesting complex ii (120 kDa, Complex from Spinacia oleracea)
Cryo-EM structure of in vitro reconstituted LHCII with C1 symmetry
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 heavy chain (24 kDa, Protein from Mus musculus)
- Magnesium transporter mgte (19 kDa, Protein from Thermus thermophilus HB8)
- Fab light chain (23 kDa, Protein from Mus musculus)
- Mgte-fab complex (Complex from Thermus thermophilus)
Structure of human cardiac thin filament in the calcium free state
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 6kn7
Q-score: 0.127
Nat Commun (2020) 11 pp. 153-153 [ DOI: doi:10.1038/s41467-019-14008-1 Pubmed: 31919429 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cardiac muscle thin filament in the calcium free state (Complex from Oryctolagus cuniculus)
- Troponin c, slow skeletal and cardiac muscles (18 kDa, Protein from Homo sapiens)
- Tropomyosin alpha-1 chain (3 kDa, Protein from Homo sapiens)
- Troponin i, cardiac muscle (19 kDa, Protein from Homo sapiens)
- Tropomyosin alpha-1 chain (31 kDa, Protein from Homo sapiens)
- Tropomyosin, troponin (Complex)
- Troponin t, cardiac muscle (23 kDa, Protein from Homo sapiens)
- Actin, alpha skeletal muscle (Complex)
- Actin, alpha skeletal muscle (41 kDa, Protein from Oryctolagus cuniculus)
Structure of human cardiac thin filament in the calcium bound state
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6kn8
Q-score: 0.127
Nat Commun (2020) 11 pp. 153-153 [ DOI: doi:10.1038/s41467-019-14008-1 Pubmed: 31919429 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Troponin t, cardiac muscle (21 kDa, Protein from Homo sapiens)
- Cardiac muscle thin filament in the calcium bound state (Complex from Oryctolagus cuniculus)
- Troponin c, slow skeletal and cardiac muscles (18 kDa, Protein from Homo sapiens)
- Troponin i, cardiac muscle (14 kDa, Protein from Homo sapiens)
- Tropomyosin alpha-1 chain (3 kDa, Protein from Homo sapiens)
- Tropomyosin alpha-1 chain (31 kDa, Protein from Homo sapiens)
- Tropomyosin, troponin (Complex)
- Actin, alpha skeletal muscle (Complex)
- Actin, alpha skeletal muscle (41 kDa, Protein from Oryctolagus cuniculus)
The 7 angstrom resolution CryoEM map of the bacterial flagellar polyrod
Resolution: 7.4 Å
EM Method: Helical reconstruction
Fitted PDBs: 5wrh
Q-score: 0.155
Fujii T, Kato T, Hiraoka KD, Miyata T, Minamino T, Chevance FF, Hughes KT, Namba K
Nat Commun (2017) 8 pp. 14276-14276 [ DOI: doi:10.1038/ncomms14276 Pubmed: 28120828 ]
The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 angstrom.
Resolution: 5.2 Å
EM Method: Helical reconstruction
Fitted PDBs: 5h53
Q-score: 0.114
Nat Commun (2017) 8 pp. 13969-13969 [ DOI: doi:10.1038/ncomms13969 Pubmed: 28067235 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin, alpha skeletal muscle (41 kDa, Protein from Rabbit)
- Actomyosin rigor complex (Complex from Oryctolagus cuniculus)
- Myosin light chain 1/3, skeletal muscle isoform (17 kDa, Protein from Rabbit)
- Myosin regulatory light chain 2, skeletal muscle isoform type 1 (16 kDa, Protein from Rabbit)
- Skeletal muscle myosin heavy chain myhc-eo/iil (96 kDa, Protein from Rabbit)
Electron cryo-microscopy of DNGR-1 in complex with F-actin
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 3j82
Q-score: 0.134