HURP(65-174) bound to GMPCPP-stabilized microtubule
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9duq
Q-score: 0.479
Valdez VA, Ma M, Gouveia B, Zhang R, Petry S
Nat Commun (2024) 15 pp. 9689-9689 [ DOI: doi:10.1038/s41467-024-53630-6 Pubmed: 39516491 ]
- Magnesium ion (24 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- Hurp(65-174) bound to gmpcpp-stabilized microtubule (Complex from Sus scrofa)
- Tubulin alpha chain (48 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Disks large-associated protein 5 (5 kDa, Protein from Homo sapiens)
Cryo-EM structure of Thogoto virus polymerase in a transcription initiation conformation
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8z8x
Q-score: 0.525
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in a transcription initiation conformation (Complex from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in transcription initiation conformation 2
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8z90
Q-score: 0.55
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Cryo-em structure of thogoto virus polymerase in transcription initiation conformation 2 (Complex from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of PAO1-ImcA with GMPCPP
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8wcn
Q-score: 0.362
Zhan X, Zhang K, Wang C, Fan Q, Tang X, Zhang X, Wang K, Fu Y, Liang H
Nat Commun (2024) 15 pp. 1860-1860 [ DOI: doi:10.1038/s41467-024-46149-3 Pubmed: 38424057 ]
- Magnesium ion (24 Da, Ligand)
- Ggdef domain-containing protein (Complex from Pseudomonas aeruginosa)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Diguanylate cyclase (51 kDa, Protein from Pseudomonas aeruginosa)
Tilapia Lake Virus polymerase in vRNA pre-termination state (transcriptase conformation)
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8qz8
Q-score: 0.531
Arragain B, Pelosse M, Thompson A, Cusack S
Nat Commun (2023) 14 pp. 8145-8145 [ Pubmed: 38066000 DOI: doi:10.1038/s41467-023-44044-x ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Rna-dependent rna polymerase (53 kDa, Protein from Tilapia lake virus)
- Putative pb1 (57 kDa, Protein from Tilapia lake virus)
- Transcription-like product (10 kDa, RNA from Tilapia lake virus)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Tilapia lake virus polymerase heterotrimeric complex (Complex from Tilapia lake virus)
- Polymerase acidic protein (pa-like) (47 kDa, Protein from Tilapia lake virus)
- Template vrna_s loop (40-mer) (12 kDa, RNA from Tilapia lake virus)
Tubulin heterodimer structure of GMPCPP state in solution
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7ysn
Q-score: 0.355
Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW
Nat Commun (2023) 14 pp. 5980-5980 [ Pubmed: 37749104 DOI: doi:10.1038/s41467-023-41615-w ]
- Tubulin beta chain (49 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin alpha-1b chain (50 kDa, Protein from Sus scrofa)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Tubulin heterodimer structure of gmpcpp state in solution (110 kDa, Complex from Sus scrofa)
Cryo-EM structure of KpFtsZ single filament
Resolution: 3.03 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ibn
Q-score: 0.36
Fujita J, Amesaka H, Yoshizawa T, Hibino K, Kamimura N, Kuroda N, Konishi T, Kato Y, Hara M, Inoue T, Namba K, Tanaka SI, Matsumura H
Nat Commun (2023) 14 pp. 4073-4073 [ Pubmed: 37429870 DOI: doi:10.1038/s41467-023-39807-5 ]
- Cell division protein ftsz (40 kDa, Protein from Klebsiella pneumoniae)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Kpftsz (Complex from Klebsiella pneumoniae)
- Cryo-em structure of kpftsz single filament (Complex)
Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8cas
Q-score: 0.366
Ikeuchi K, Ivic N, Buschauer R, Cheng J, Frohlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R
Nat Commun (2023) 14 pp. 2730-2730 [ Pubmed: 37169754 DOI: doi:10.1038/s41467-023-38161-w ]
- Eukaryotic translation initiation factor 3 subunit a (110 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit i (38 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- Trna (24 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s31 (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Protein-synthesizing gtpase (57 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Mrna (2 kDa, RNA from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Methionine (149 Da, Ligand)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui3 isoform 1 (31 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit c (93 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit b (88 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l40-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui2 isoform 1 (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit g (30 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s26-a (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 4c (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Tif5 isoform 1 (45 kDa, Protein from Saccharomyces cerevisiae W303)
- Rli1 isoform 1 (68 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- Yeast native 48s initiation complex (partial) with deubiquitinating enzyme otu2 bound to ubiquitinated es7 (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)
P. berghei kinesin-8B motor domain in AMPPNP state bound to tubulin dimer
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7z2b
Q-score: 0.367
Liu T, Shilliday F, Cook AD, Zeeshan M, Brady D, Tewari R, Sutherland CJ, Roberts AJ, Moores CA
Nat Commun (2022) 13 pp. 6988-6988 [ DOI: doi:10.1038/s41467-022-34710-x Pubmed: 36384964 ]
- Magnesium ion (24 Da, Ligand)
- Kinesin-8, putative (38 kDa, Protein from Plasmodium berghei)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- P. berghei kinesin-8b motor domain in amppnp state bound to tubulin dimer (Complex from Plasmodium berghei)
- Detyrosinated tubulin alpha-1b chain (47 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
P. berghei kinesin-8B motor domain in no nucleotide state bound to tubulin dimer
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7z2a
Q-score: 0.253
Liu T, Shilliday F, Cook AD, Zeeshan M, Brady D, Tewari R, Sutherland CJ, Roberts AJ, Moores CA
Nat Commun (2022) 13 pp. 6988-6988 [ DOI: doi:10.1038/s41467-022-34710-x Pubmed: 36384964 ]
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- Kinesin-8, putative (39 kDa, Protein from Plasmodium berghei)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Detyrosinated tubulin alpha-1b chain (47 kDa, Protein from Sus scrofa)
- P. berghei kinesin-8b motor domain in no nucleotide state bound to tubulin dimer (Complex from Plasmodium berghei)
- Magnesium ion (24 Da, Ligand)