Resolution: 3.9 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x54
Q-score: 0.375
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cbg-parm filament with adp (Complex from Clostridium botulinum)
- Magnesium ion (24 Da, Ligand)
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum Bf)
A CBg-ParM filament with GTP and a short incubation time
Resolution: 8.6 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x55
Q-score: 0.168
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x56
Q-score: 0.486
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Cbg-parm filament with gdp (Complex from Clostridium botulinum)
- Magnesium ion (24 Da, Ligand)
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum Bf)
A CBg-ParM filament with GTP or GDPPi
Resolution: 6.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x59
Q-score: 0.189
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cbg-parm filament with gtp or gdppi (Complex from Clostridium botulinum)
Cryo-EM structure of phosphoketolase from Bifidobacterium longum
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 6lxv
Q-score: 0.763
Nakata K, Miyazaki N, Yamaguchi H, Hirose M, Kashiwagi T, Kutumbarao NHV, Miyashita O, Tama F, Miyano H, Mizukoshi T, Iwasaki K
J Struct Biol (2022) 214 pp. 107842-107842 [ DOI: doi:10.1016/j.jsb.2022.107842 Pubmed: 35181457 ]
- Thiamine diphosphate (425 Da, Ligand)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Phosphoketolase with thiamine-diphophate (Complex from Bifidobacterium longum subsp. longum F8)
- Phosphoketolase (93 kDa, Protein from Bifidobacterium longum subsp. longum F8)
Cryo-EM structure of T=3 Penaeus vannamei nodavirus
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6ab6
Q-score: 0.505
Chen NC, Yoshimura M, Miyazaki N, Guan HH, Chuankhayan P, Lin CC, Chen SK, Lin PJ, Huang YC, Iwasaki K, Nakagawa A, Chan SI, Chen CJ
Commun Biol (2019) 2 pp. 72-72 [ DOI: doi:10.1038/s42003-019-0311-z Pubmed: 30820467 ]
- Calcium ion (40 Da, Ligand)
- Capsid protein (40 kDa, Protein from Penaeus vannamei nodavirus)
- Penaeus vannamei nodavirus (Virus from Penaeus vannamei nodavirus)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6rvv
Q-score: 0.445
Malay AD, Miyazaki N, Biela A, Chakraborti S, Majsterkiewicz K, Stupka I, Kaplan CS, Kowalczyk A, Piette BMAG, Hochberg GKA, Wu D, Wrobel TP, Fineberg A, Kushwah MS, Kelemen M, Vavpetic P, Pelicon P, Kukura P, Benesch JLP, Iwasaki K, Heddle JG
Nature (2019) 569 pp. 438-442 [ Pubmed: 31068697 DOI: doi:10.1038/s41586-019-1185-4 ]
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6rvw
Q-score: 0.449
Malay AD, Miyazaki N, Biela A, Chakraborti S, Majsterkiewicz K, Stupka I, Kaplan CS, Kowalczyk A, Piette BMAG, Hochberg GKA, Wu D, Wrobel TP, Fineberg A, Kushwah MS, Kelemen M, Vavpetic P, Pelicon P, Kukura P, Benesch JLP, Iwasaki K, Heddle JG
Nature (2019) 569 pp. 438-442 [ Pubmed: 31068697 DOI: doi:10.1038/s41586-019-1185-4 ]
Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1
Resolution: 21.0 Å
EM Method: Single-particle
Fitted PDBs: 5gje
Q-score: 0.027
Matoba K, Mihara E, Tamura-Kawakami K, Miyazaki N, Maeda S, Hirai H, Thompson S, Iwasaki K, Takagi J
Cell Rep (2017) 18 pp. 32-40 [ DOI: doi:10.1016/j.celrep.2016.12.017 Pubmed: 28052259 ]
- Phosphate ion (94 Da, Ligand)
- Lrp6 ectodomain (Complex)
- Glycerol (92 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dickkopf-related protein 1 (9 kDa, Protein from Homo sapiens)
- Low-density lipoprotein receptor-related protein 6 (69 kDa, Protein from Homo sapiens)
- Human dickkopf-related protein1 (Complex)
- Low-density lipoprotein receptor-related protein 6 (69 kDa, Protein from Homo sapiens)
- Human lrp6 ectodomain complexed with full length of dkk1 (210 kDa, Complex from Homo sapiens)
- Water (18 Da, Ligand)