A designed tetrahedral protein scaffold - DARP14
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8vdz
Q-score: 0.626
Int J Mol Sci (2024) 25 [ Pubmed: 38891853 DOI: doi:10.3390/ijms25115665 ]
- Subunit b (12 kDa, Protein from synthetic construct)
- Subunit b in a designed protein scaffold called darp14 (Complex from synthetic construct)
- Subunit a (15 kDa, Protein from synthetic construct)
- A12b12 tetrahedral complex of a designed protein scaffold called darp14 (Complex from synthetic construct)
- Subunit a in a designed protein scaffold called darp14 (Complex from synthetic construct)
Int J Mol Sci (2024) 25 [ Pubmed: 38891853 DOI: doi:10.3390/ijms25115665 ]
Trimeric component of a designed scaffold called DARP14
Int J Mol Sci (2024) 25 [ Pubmed: 38891853 DOI: doi:10.3390/ijms25115665 ]
- Subunit a with darpin in a designed protein scaffold called darp14 (Complex from synthetic construct)
- Trimeric component of a tetrahedral complex of a designed protein scaffold called darp14 (Complex from synthetic construct)
- Subunit b in a designed protein scaffold called darp14 (Complex from synthetic construct)
A DARPin displayed on a designed tetrahedral protein scaffold
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8ve7
Q-score: 0.323
Int J Mol Sci (2024) 25 [ Pubmed: 38891853 DOI: doi:10.3390/ijms25115665 ]
Int J Mol Sci (2024) 25 [ Pubmed: 38891853 DOI: doi:10.3390/ijms25115665 ]
Cryo-EM structure of SaCas9-sgRNA-DNA ternary complex
Du W, Zhu H, Qian J, Xue D, Zheng S, Huang Q
Int J Mol Sci (2023) 24 [ DOI: doi:10.3390/ijms24021204 Pubmed: 36674715 ]
- Single-guide rna (sgrna) (RNA from synthetic construct)
- Sacas9 (Complex)
- Target dna strand(ts) (DNA from synthetic construct)
- Non-target dna strand (nts) (DNA from synthetic construct)
- Sacas9 (Protein from Staphylococcus aureus)
- Sacas9-sgrna-target dna ternary complex (Complex from Staphylococcus aureus)
- Sgrna-target dna (Complex)
SsoMCM hexamer bound to Mg/ADP-BeFx and 12-mer oligo-dT. Class 1
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8eaf
Q-score: 0.497
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ssomcm hexamer bound to mg/adp-befx and 12-mer oligo-dt. class 1. (Complex from Saccharolobus solfataricus P2)
- 12-mer oligo dt (3 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
SsoMCM hexamer bound to Mg/ADP-BeFx and 12-mer oligo-dT. Class 2
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8eag
Q-score: 0.432
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 12-mer oligo-dt (3 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Ssomcm hexamer bound to mg/adp-befx and 12-mer oligo-dt. class 2. (Complex from Saccharolobus solfataricus P2)
- Water (18 Da, Ligand)
SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 1
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8eah
Q-score: 0.509
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 16-mer oligo-dt (4 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Ssomcm hexamer bound to mg/adp-befx and 16-mer oligo-dt class 1 (Complex from Saccharolobus solfataricus P2)
SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 2
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8eai
Q-score: 0.465
Meagher M, Myasnikov A, Enemark EJ
Int J Mol Sci (2022) 23 [ Pubmed: 36499022 DOI: doi:10.3390/ijms232314678 ]
- [[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium (492 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Mcm hexamer bound to mg/adp-befx and 16-mer oligo-dt. class 2 (Complex from Saccharolobus solfataricus P2)
- 16-mer oligo-dt (4 kDa, DNA from synthetic construct)
- Minichromosome maintenance protein mcm (68 kDa, Protein from Saccharolobus solfataricus P2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)