Minus end of the vertebrate gamma-tubulin ring complex-capped microtubule
Resolution: 23.0 Å
EM Method: Single-particle
Fitted PDBs: 9eok
Q-score: 0.036
Vermeulen BJ, Bohler A, Gao Q, Neuner A, Zupa E, Chu Z, Wurtz M, Jakle U, Gruss OJ, Pfeffer S, Schiebel E
EMBO J (2024) 43 pp. 2062-2085 [ DOI: doi:10.1038/s44318-024-00087-4 Pubmed: 38600243 ]
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Tubulin alpha chain (50 kDa, Protein from Xenopus laevis)
- Minus end of the vertebrate gamma-tubulin ring complex-capped microtubule (Complex from Xenopus laevis)
- Taxol (853 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tubulin beta-4 chain (49 kDa, Protein from Xenopus laevis)
Resolution: 26.8 Å
EM Method: Subtomogram averaging
Fitted PDBs: 8r1a
Q-score: 0.03
Weismehl M, Chu X, Kutsch M, Lauterjung P, Herrmann C, Kudryashev M, Daumke O
EMBO J (2024) 43 pp. 615-636 [ DOI: doi:10.1038/s44318-023-00023-y Pubmed: 38267655 ]
- Aluminum fluoride (83 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanylate binding protein 1 (69 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Membrane-bound oligomer of human guanylate-binding protein 1 (gbp1) (Complex from Homo sapiens)
Sub-tomogram averaged map of full-length post-fusion CHIKV E1 glycoprotein trimer
Resolution: 27.2 Å
EM Method: Subtomogram averaging
Fitted PDBs: 8d87
Q-score: 0.029
Mangala Prasad V, Blijleven JS, Smit JM, Lee KK
Nat Commun (2022) 13 pp. 4772-4772 [ Pubmed: 35970990 DOI: doi:10.1038/s41467-022-32431-9 ]
- Sub-tomogram averaged map of post-fusion e1 glycoprotein trimer from chikungunya virus (150 kDa, Complex from Chikungunya virus strain S27-African prototype)
- Phosphate ion (94 Da, Ligand)
- Spike glycoprotein e1 (42 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Bromide ion (79 Da, Ligand)
- Holmium atom (164 Da, Ligand)
- Water (18 Da, Ligand)
Composite structure of dynein-dynactin-BICDR on microtubules
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 7z8f
Q-score: 0.215
Nature (2022) 610 pp. 212-216 [ DOI: doi:10.1038/s41586-022-05186-y Pubmed: 36071160 ]
- Arp11 (46 kDa, Protein from Sus scrofa)
- Actin, cytoplasmic 1 (41 kDa, Protein from Sus scrofa)
- Dynein, cytoplasmic 1 (1 MDa, Cellular component from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Dynactin subunit 2 (44 kDa, Protein from Sus scrofa)
- Complex of dynein, dynactin, and bicdr1 bound to microtubules (4 MDa, Complex)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Dynactin subunit 4 (52 kDa, Protein from Sus scrofa)
- Cytoplasmic dynein 1 intermediate chain 2 (71 kDa, Protein from Homo sapiens)
- F-actin capping protein beta subunit (30 kDa, Protein from Sus scrofa)
- Bicd family-like cargo adapter 1 (65 kDa, Protein from Mus musculus)
- Dynactin (1 MDa, Cellular component from Sus scrofa)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Dynactin subunit 5 (20 kDa, Protein from Sus scrofa)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynein light chain roadblock-type 1 (10 kDa, Protein from Homo sapiens)
- Capping protein (actin filament) muscle z-line, alpha 1 (33 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynactin subunit 3 (21 kDa, Protein from Sus scrofa)
- Bicdr1 (130 kDa, Cellular component from Mus musculus)
- Dynactin subunit 1 (142 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dynactin 6 (20 kDa, Protein from Sus scrofa)
SAGA-TBP filtered to show the position of the DUB domain
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 6tbm
Q-score: 0.08
Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A
Nature (2020) 577 pp. 711-716 [ DOI: doi:10.1038/s41586-020-1944-2 Pubmed: 31969704 ]
- Subunit (60 kda) of tfiid and saga complexes (54 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcriptional coactivator hfi1/ada1 (49 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Water (18 Da, Ligand)
- Saga complex (Complex from Komagataella phaffii GS115)
- Tata-box binding protein (tbp) (27 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription and mrna export factor sus1 (11 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Saga-associated factor 11 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt20 (59 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcriptional regulator involved in glucose repression of gal4p-regulated genes (81 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Ubiquitin carboxyl-terminal hydrolase (56 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of saga histone acetyltransferase complex (79 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of the saga and saga-like transcriptional regulatory complexes, interacts with spt15p to act (39 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Tata-box binding protein (tbp) (Complex from Komagataella phaffii GS115)
- Polyubiquitin-b (Complex from Homo sapiens)
- Saga bound to tbp (1 MDa, Complex)
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
- Saga component (Complex from Komagataella phaffii GS115)
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (61/68 kda) of tfiid and saga complexes (66 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt8 (34 kDa, Protein from Komagataella phaffii GS115)
- Subunit of the saga transcriptional regulatory complex, involved in proper assembly of the complex (136 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (17 kda) of tfiid and saga complexes, involved in rna polymerase ii transcription initiation (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (90 kda) of tfiid and saga complexes (80 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 6v92
Q-score: 0.053
Patel AB, Moore CM, Greber BJ, Luo J, Zukin SA, Ranish J, Nogales E
eLife (2019) 8 [ Pubmed: 31886770 DOI: doi:10.7554/eLife.54449 ]
- Rsc-ncp complex (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Unknown protein (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc14 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (4 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (2 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Uuknown protein (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Thin Filament at low calcium concentration
Resolution: 28.4 Å
EM Method: Single-particle
Fitted PDBs: 5mvy
Q-score: 0.003
J Struct Biol (2017) 197 pp. 365-371 [ DOI: doi:10.1016/j.jsb.2017.01.004 Pubmed: 28161413 ]
- Actin, alpha skeletal muscle (41 kDa, Protein from Rabbit)
- Thin filament (Complex from Oryctolagus cuniculus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Structure of the thin filament at high calcium concentration
J Struct Biol (2017) 197 pp. 365-371 [ DOI: doi:10.1016/j.jsb.2017.01.004 Pubmed: 28161413 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin, alpha skeletal muscle (41 kDa, Protein from Rabbit)
- Thin filament at high calcium concentration (Complex from Oryctolagus cuniculus)
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 [ Pubmed: 28052259 DOI: doi:10.1016/j.celrep.2016.12.017 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dickkopf-related protein 1 (9 kDa, Protein from Homo sapiens)
- Human dickkopf-related protein1 (Complex)
- Phosphate ion (94 Da, Ligand)
- Low-density lipoprotein receptor-related protein 6 (69 kDa, Protein from Homo sapiens)
- Glycerol (92 Da, Ligand)
- Human lrp6 ectodomain complexed with full length of dkk1 (210 kDa, Complex from Homo sapiens)
- Low-density lipoprotein receptor-related protein 6 (69 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Lrp6 ectodomain (Complex)
Resolution: 26.5 Å
EM Method: Single-particle
Fitted PDBs: 5lcb
Q-score: -0.012
Nielsen JT, Kulminskaya NV, Bjerring M, Linnanto JM, Ratsep M, Pedersen MO, Lambrev PH, Dorogi M, Garab G, Thomsen K, Jegerschold C, Frigaard NU, Lindahl M, Nielsen NC
Nat Commun (2016) 7 pp. 12454-12454 [ Pubmed: 27534696 DOI: doi:10.1038/ncomms12454 ]