Structure of human soluble guanylate cyclase in the NO+Rio state at 3.1 angstrom
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hbf
Q-score: 0.539
Nitric Oxide (2023) 134-135 pp. 17-22 [ DOI: doi:10.1016/j.niox.2023.03.002 Pubmed: 36972843 ]
- Methyl ~{n}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{n}-methyl-carbamate (422 Da, Ligand)
- Guanylate cyclase soluble subunit alpha-1 (77 kDa, Protein from Homo sapiens)
- Nitric oxide (30 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Human soluble guanylate cyclase (Complex from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Guanylate cyclase soluble subunit beta-1 (70 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Structure of human soluble guanylate cyclase in the NO-activated state at 3.1 angstrom
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hbh
Q-score: 0.537
Nitric Oxide (2023) 134-135 pp. 17-22 [ DOI: doi:10.1016/j.niox.2023.03.002 Pubmed: 36972843 ]
- Guanylate cyclase soluble subunit alpha-1 (77 kDa, Protein from Homo sapiens)
- Nitric oxide (30 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Human soluble guanylate cyclase (Complex from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Guanylate cyclase soluble subunit beta-1 (70 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
M. tuberculosis RNAP pause escaped complex with Bacillus subtilis NusG and GMPCPP
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8ej3
Q-score: 0.511
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ Pubmed: 36745813 DOI: doi:10.1073/pnas.2218516120 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Pause escaped transcription complex with nusg and gmpcpp (Complex from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (29-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Dna (32-mer) (12 kDa, DNA from synthetic construct)
- Rna (5'-r(p*up*cp*gp*gp*cp*ap*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (9 kDa, RNA from synthetic RNA)
M. tuberculosis RNAP paused complex with B. subtilis NusG and GMPCPP
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8exy
Q-score: 0.457
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ Pubmed: 36745813 DOI: doi:10.1073/pnas.2218516120 ]
- Rna (29-mer) (9 kDa, RNA from synthetic construct)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Pause escaped transcription complex with nusg and gmpcpp (Complex from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Zinc ion (65 Da, Ligand)
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8bf5
Q-score: 0.54
Kouba T, Dubankova A, Drncova P, Donati E, Vidossich P, Speranzini V, Pflug A, Huchting J, Meier C, De Vivo M, Cusack S
Cell Rep (2023) 42 pp. 111901-111901 [ Pubmed: 36596301 DOI: doi:10.1016/j.celrep.2022.111901 ]
- Early transcription elongation state of influenza a/h7n9 polymerase stalled with incoming gtp analogue (255 kDa, Complex from Influenza B virus (B/Memphis/13/2003))
- P1-7-methylguanosine-p3-adenosine-5',5'-triphosphate (787 Da, Ligand)
- 5' vrna (4 kDa, RNA from Influenza B virus)
- Polymerase basic protein 2 (90 kDa, Protein from Influenza B virus (B/Memphis/13/2003))
- Mrna (5 kDa, RNA from Influenza B virus)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- 3' vrna (6 kDa, RNA from Influenza B virus)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza B virus (B/Memphis/13/2003))
- Magnesium ion (24 Da, Ligand)
- Polymerase acidic protein (85 kDa, Protein from Influenza B virus (B/Memphis/13/2003))
Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7zcw
Q-score: 0.509
Ramirez-Rios S, Choi SR, Sanyal C, Blum TB, Bosc C, Krichen F, Denarier E, Soleilhac JM, Blot B, Janke C, Stoppin-Mellet V, Magiera MM, Arnal I, Steinmetz MO, Moutin MJ
J Cell Biol (2023) 222 [ DOI: doi:10.1083/jcb.202205096 Pubmed: 36512346 ]
- Tubulin alpha-1b chain (50 kDa, Protein from Homo sapiens)
- Small vasohibin-binding protein (8 kDa, Protein from Homo sapiens)
- Vash2-svbp complex bound to the microtubule (380 kDa, Complex from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin beta-2b chain (49 kDa, Protein from Homo sapiens)
- Tubulinyl-tyr carboxypeptidase 2 (40 kDa, Protein from Homo sapiens)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
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)
P. falciparum kinesin-8B motor domain in no nucleotide bound to tubulin dimer
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7z2c
Q-score: 0.296
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 [ Pubmed: 36384964 DOI: doi:10.1038/s41467-022-34710-x ]
- Magnesium ion (24 Da, Ligand)
- Kinesin-like protein (39 kDa, Protein from Plasmodium falciparum)
- P. falciparum kinesin-8b motor domain in no nucleotide state bound to tubulin dimer (Complex from Plasmodium berghei)
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Detyrosinated tubulin alpha-1b chain (47 kDa, Protein from Sus scrofa)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7quq
Q-score: 0.427
Wagstaff JM, Planelles-Herrero VJ, Sharov G, Alnami A, Kozielski F, Derivery E, Lowe J
Sci Adv (2023) 9 pp. eadf3021-eadf3021 [ DOI: doi:10.1126/sciadv.adf3021 Pubmed: 36989372 ]
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Tubulin beta (46 kDa, Protein from Prosthecobacter dejongeii)
- Btubab heterodimer (Complex from Drosophila melanogaster)
- Tubulin domain-containing protein (51 kDa, Protein from Prosthecobacter dejongeii)