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Cryo-EM structure of tetrameric human SAMHD1 with dApNHpp
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8qxj
Q-score: 0.574
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA
Nat Commun (2024) 15 pp. 3775-3775 [ DOI: doi:10.1038/s41467-024-48237-w Pubmed: 38710701 ]
- Fe (iii) ion (55 Da, Ligand)
- Homotetramer of samhd1 (Complex from Homo sapiens)
- 2'-deoxy-5'-o-[(r)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (490 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
Cryo-EM structure of tetrameric human SAMHD1 State I - Tense
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8qxk
Q-score: 0.62
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA
Nat Commun (2024) 15 pp. 3775-3775 [ DOI: doi:10.1038/s41467-024-48237-w Pubmed: 38710701 ]
- Fe (iii) ion (55 Da, Ligand)
- Homotetramer of samhd1 (Complex from Homo sapiens)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
Cryo-EM structure of tetrameric human SAMHD1 State II - Hemi-relaxed
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 8qxl
Q-score: 0.541
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA
Nat Commun (2024) 15 pp. 3775-3775 [ DOI: doi:10.1038/s41467-024-48237-w Pubmed: 38710701 ]
- Fe (iii) ion (55 Da, Ligand)
- Homotetramer of samhd1 (Complex from Homo sapiens)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Triphosphate (257 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 2'-deoxycytidine (227 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
Cryo-EM structure of tetrameric human SAMHD1 State III - Relaxed
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8qxm
Q-score: 0.573
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA
Nat Commun (2024) 15 pp. 3775-3775 [ DOI: doi:10.1038/s41467-024-48237-w Pubmed: 38710701 ]
- Fe (iii) ion (55 Da, Ligand)
- Homotetramer of samhd1 (Complex from Homo sapiens)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
Cryo-EM structure of tetrameric human SAMHD1 State IV - Depleted relaxed
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8qxn
Q-score: 0.459
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA
Nat Commun (2024) 15 pp. 3775-3775 [ DOI: doi:10.1038/s41467-024-48237-w Pubmed: 38710701 ]
- Fe (iii) ion (55 Da, Ligand)
- Homotetramer of samhd1 (Complex from Homo sapiens)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
Cryo-EM structure of tetrameric human SAMHD1 State V - Depleted relaxed
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8qxo
Q-score: 0.417
Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA
Nat Commun (2024) 15 pp. 3775-3775 [ DOI: doi:10.1038/s41467-024-48237-w Pubmed: 38710701 ]
- Fe (iii) ion (55 Da, Ligand)
- Homotetramer of samhd1 (Complex from Homo sapiens)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
Human RAD52 open ring - ssDNA complex
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8rjw
Q-score: 0.512
Liang CC, Greenhough LA, Masino L, Maslen S, Bajrami I, Tuppi M, Skehel M, Taylor IA, West SC
Nature (2024) 629 pp. 697-703 [ DOI: doi:10.1038/s41586-024-07347-7 Pubmed: 38658755 ]
- Water (18 Da, Ligand)
- Ssdna (6 kDa, DNA from Homo sapiens)
- Dna repair protein rad52 homolog (46 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Open ring conformation of human rad52 in complex with ssdna (Complex from Homo sapiens)
MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7z1z
Q-score: 0.19
Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P
Nat Commun (2022) 13 pp. 2416- [ DOI: doi:10.1038/s41467-022-29928-8 ]
- Pc4 and sfrs1-interacting protein (11 kDa, Protein from Homo sapiens)
- Pol polyprotein (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Mvv stc intasome in complex with ledgf (480 kDa, Complex from Visna/maedi virus EV1 KV1772)
- Dna (37-mer) (15 kDa, DNA from DNA molecule)
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(p*tp*tp*gp*ap*tp*tp*ap*gp*gp*gp*tp*g)-3') (7 kDa, DNA from DNA molecule)
- Dna (5'-d(*gp*cp*tp*gp*cp*gp*ap*gp*ap*tp*cp*cp*gp*cp*tp*cp*cp*gp*gp*tp*g)-3') (7 kDa, DNA from DNA molecule)
MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 7u32
Q-score: 0.256
Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P
Nat Commun (2022) 13 pp. 2416-2416 [ Pubmed: 35504909 DOI: doi:10.1038/s41467-022-29928-8 ]
- Calcium ion (40 Da, Ligand)
- Integrase (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Zinc ion (65 Da, Ligand)
- Dna ev272 (8 kDa, DNA from synthetic construct)
- Dna ev273 (8 kDa, DNA from synthetic construct)
- Mvv cleaved synaptic complex intasome (480 kDa, Complex from Streptomyces griseus)