Resolution: 5.3 Å
EM Method: Single-particle
Fitted PDBs: 8ytc
Q-score: 0.09
Tan Y, Li J, Zhang S, Zhang Y, Zhuo Z, Ma X, Yin Y, Jiang Y, Cong Y, Meng G
Cell Discov (2024) 10 pp. 118-118 [ Pubmed: 39587079 DOI: doi:10.1038/s41421-024-00735-3 ]
- Promyelocytic leukemia protein (Complex from Homo sapiens)
- Protein pml (23 kDa, Protein from Homo sapiens)
human NaS1 intermediate state 2
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8y5w
Q-score: 0.579
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
- Membrane sodium anion transproter 2 (Complex from Homo sapiens)
- Sodium ion (22 Da, Ligand)
human NaS1 intermediate state 3
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8y5x
Q-score: 0.484
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Membrane sodium anion transproter 3 (Cellular component from Homo sapiens)
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
- Sodium ion (22 Da, Ligand)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8y5y
Q-score: 0.443
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Membrane sodium anion transproter out (Complex from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8y5z
Q-score: 0.474
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Membrane sodium anion transproter in (Complex from Homo sapiens)
Architecture of the spinach plastid-encoded RNA polymerase
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8xzv
Q-score: 0.444
Wang T, Wang GL, Fang Y, Zhang Y, Peng W, Zhou Y, Zhang A, Yu LJ, Lu C
Nat Commun (2024) 15 pp. 9838-9838 [ Pubmed: 39537621 DOI: doi:10.1038/s41467-024-54266-2 ]
- Ptac3 (101 kDa, Protein from Spinacia oleracea)
- Spinach plastid-encoded rna polymerase (960 kDa, Complex from Spinacia oleracea)
- Dna-directed rna polymerase subunit beta'' (154 kDa, Protein from Spinacia oleracea)
- Ptac18 (17 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 14 isoform x2 (56 kDa, Protein from Spinacia oleracea)
- Superoxide dismutase (31 kDa, Protein from Spinacia oleracea)
- Fructokinase-like 2, chloroplastic isoform x2 (65 kDa, Protein from Spinacia oleracea)
- Fructokinase-like 1, chloroplastic (53 kDa, Protein from Spinacia oleracea)
- Fe (iii) ion (55 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Spinacia oleracea)
- Dna-directed rna polymerase subunit beta (121 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 10 (80 kDa, Protein from Spinacia oleracea)
- Ptac6 (37 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 7 (19 kDa, Protein from Spinacia oleracea)
- Superoxide dismutase (31 kDa, Protein from Spinacia oleracea)
- Dna-directed rna polymerase subunit beta' (78 kDa, Protein from Spinacia oleracea)
- Mure (85 kDa, Protein from Spinacia oleracea)
- Thioredoxin-like protein citrx, chloroplastic (20 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 12 (59 kDa, Protein from Spinacia oleracea)
pRib-ADP bound OsEDS1-PAD4-ADR1 complex
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8zf0
Q-score: 0.443
Wu Y, Xu W, Zhao G, Lei Z, Li K, Liu J, Huang S, Wang J, Zhong X, Yin X, Wang Y, Zhang H, He Y, Ye Z, Meng Y, Chang X, Lin H, Wang X, Gao Y, Chai J, Parker JE, Deng Y, Zhang Y, Gao M, He Z
Science (2024) 386 pp. 1405-1412 [ DOI: doi:10.1126/science.adr2138 Pubmed: 39509474 ]
- Rpw8 domain-containing protein (96 kDa, Protein from Oryza sativa Japonica Group)
- [(2r,3r,4r,5r)-5-(6-aminopurin-9-yl)-4-[(2s,3r,4s,5r)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate (639 Da, Ligand)
- Lipase-like pad4 (71 kDa, Protein from Oryza sativa Japonica Group)
- Eds1 (68 kDa, Protein from Oryza sativa Japonica Group)
- Prib-adp bound oseds1-pad4-adr1 complex (Complex from Oryza sativa subsp. japonica)
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
Cryo-EM density map of DNMT3A1-DNMT3L on a human H2AKc119ub nucleosome at 5.1 A resolution
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h2ak119c (Protein from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Histone h3 (Protein from Homo sapiens)
- Dnmt3a1 (Protein from Homo sapiens)
- Dnmt3l (Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- 195bp widom601 dna (DNA from synthetic construct)
- Ubiquitin (Protein from Homo sapiens)
- Histone h2b (Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)