Lee S, Kibler RD, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Stoddard B, Baker D
To Be Published
- Icos(t=4)-4 chain ho (Protein from synthetic construct)
- Icos(t=4)-4 chain b (Protein from synthetic construct)
- Icos(t=4)-4 (Complex from synthetic construct)
- Icos(t=4)-4 chain c (Protein from synthetic construct)
- Icos(t=4)-4 chain a (Protein from synthetic construct)
CryoEM map of a T=1 off-target state of design Ico(T=4)-4
Lee S, Kibler RD, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Stoddard B, Baker D
To Be Published
Lee S, Kibler RD, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Stoddard B, Baker D
To Be Published
- Oct(t=4)-3 (Complex from synthetic construct)
- Oct(t=4)-3 chain a (Protein from synthetic construct)
- Oct(t=4)-3 chain c (Protein from synthetic construct)
- Oct(t=4)-3 chain ho (Protein from synthetic construct)
- Oct(t=4)-3 chain b (Protein from synthetic construct)
CryoEM map of a T=1 off-target state of design Oct(T=4)-3
Lee S, Kibler RD, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Stoddard B, Baker D
To Be Published
- Oct(t=4)-3 (Complex from synthetic construct)
Backbone model of de novo-designed chlorophyll-binding nanocage O32-15
Resolution: 6.5 Å
EM Method: Single-particle
Fitted PDBs: 8glt
Q-score: 0.213
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D
Nat Chem Biol (2024) 20 pp. 906-915 [ Pubmed: 38831036 DOI: doi:10.1038/s41589-024-01626-0 ]
Chlorophyll-binding region of de novo-designed nanocage O32-15
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D
Nat Chem Biol (2024) 20 pp. 906-915 [ Pubmed: 38831036 DOI: doi:10.1038/s41589-024-01626-0 ]
Type IIS Restriction Endonuclease PaqCI, DNA bound
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8epx
Q-score: 0.545
Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL
Nucleic Acids Res (2023) 51 pp. 4467-4487 [ DOI: doi:10.1093/nar/gkad228 Pubmed: 36987874 ]
- Dna 4b (4 kDa, DNA from DNA molecule)
- Dna 3a (5 kDa, DNA from DNA molecule)
- Dna 3b (5 kDa, DNA from DNA molecule)
- Dna 1a (7 kDa, DNA from DNA molecule)
- Calcium ion (40 Da, Ligand)
- Homotetramer paqci with associated dna duplexes (Complex from Paucibacter aquatile)
- Dna 2a (4 kDa, DNA from DNA molecule)
- Dna 2b (5 kDa, DNA from DNA molecule)
- Dna 1b (6 kDa, DNA from DNA molecule)
- Type iis restriction endonuclease paqci (56 kDa, Protein from Paucibacter aquatile)
- Dna 4a (4 kDa, DNA from DNA molecule)
Human CTPS1 bound to UTP, AMPPNP, and glutamine
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7mgz
Q-score: 0.55
Lynch EM, DiMattia MA, Albanese S, van Zundert GCP, Hansen JM, Quispe JD, Kennedy MA, Verras A, Borrelli K, Toms AV, Kaila N, Kreutter KD, McElwee JJ, Kollman JM
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2107968118 Pubmed: 34583994 ]
- Ctps1 tetramer (Complex from Homo sapiens)
- Ctp synthase 1 (66 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Glutamine (146 Da, Ligand)
- Uridine 5'-triphosphate (484 Da, Ligand)
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 7mh0
Q-score: 0.205
Lynch EM, DiMattia MA, Albanese S, van Zundert GCP, Hansen JM, Quispe JD, Kennedy MA, Verras A, Borrelli K, Toms AV, Kaila N, Kreutter KD, McElwee JJ, Kollman JM
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2107968118 Pubmed: 34583994 ]
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Ctps1 tetramer (Complex from Homo sapiens)
- Ctp synthase 1 (66 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7mh1
Q-score: 0.536
Lynch EM, DiMattia MA, Albanese S, van Zundert GCP, Hansen JM, Quispe JD, Kennedy MA, Verras A, Borrelli K, Toms AV, Kaila N, Kreutter KD, McElwee JJ, Kollman JM
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2107968118 Pubmed: 34583994 ]
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Ctps2 tetramer (Complex from Homo sapiens)
- Ctp synthase 2 (65 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)