Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8vg0
Q-score: 0.482
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Maltose/maltodextrin-binding periplasmic protein,transcription factor gata-4 (87 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (159-mer) (57 kDa, DNA from synthetic construct)
- Dna (159-mer) (57 kDa, DNA from synthetic construct)
- Gata4 in complex with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8vg1
Q-score: 0.541
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Maltose/maltodextrin-binding periplasmic protein,transcription factor gata-4 (87 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Foxa1 and gata4 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Echovirus3 empty compacted particle
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7eai
Q-score: 0.488
Feng R, Wang L, Shi D, Zheng B, Zhang L, Hou H, Xia D, Cui L, Wang X, Xu S, Wang K, Zhu L
Cell Discov (2021) 7 pp. 35-35 [ Pubmed: 34035235 DOI: doi:10.1038/s41421-021-00264-3 ]
- Capsid protein vp3 (26 kDa, Protein from Echovirus E3)
- Capsid protein vp0 (36 kDa, Protein from Echovirus E3)
- Sphingosine (299 Da, Ligand)
- Echovirus e3 (Virus from Echovirus E3)
- Capsid protein vp1 (32 kDa, Protein from Echovirus E3)
Echovirus3 full particle in complex with 5G3 fab
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7eak
Q-score: 0.453
Feng R, Wang L, Shi D, Zheng B, Zhang L, Hou H, Xia D, Cui L, Wang X, Xu S, Wang K, Zhu L
Cell Discov (2021) 7 pp. 35-35 [ Pubmed: 34035235 DOI: doi:10.1038/s41421-021-00264-3 ]
- Capsid protein vp4 (7 kDa, Protein from Echovirus E3)
- Heavy chain of 5g3 fab (12 kDa, Protein from Mus musculus)
- Capsid protein vp2 (29 kDa, Protein from Echovirus E3)
- Echovirus e3 in complex with 5g3 fab (Complex)
- Light chain of 5g3 fab (12 kDa, Protein from Mus musculus)
- 5g3 fab (Complex from Mus musculus)
- Echovirus e3 (Complex from Echovirus E3)
- Capsid protein vp3 (26 kDa, Protein from Echovirus E3)
- Sphingosine (299 Da, Ligand)
- Capsid protein vp1 (32 kDa, Protein from Echovirus E3)
- Myristic acid (228 Da, Ligand)
SARS-CoV-2 spike protein and P17 fab complex with one RBD in close state
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7cwl
Q-score: 0.257
Yao H, Sun Y, Deng YQ, Wang N, Tan Y, Zhang NN, Li XF, Kong C, Xu YP, Chen Q, Cao TS, Zhao H, Yan X, Cao L, Lv Z, Zhu D, Feng R, Wu N, Zhang W, Hu Y, Chen K, Zhang RR, Lv Q, Sun S, Zhou Y, Yan R, Yang G, Sun X, Liu C, Lu X, Cheng L, Qiu H, Huang XY, Weng T, Shi D, Jiang W, Shao J, Wang L, Zhang J, Jiang T, Lang G, Qin CF, Li L, Wang X
Cell Res (2021) 31 pp. 25-36 [ Pubmed: 33262452 DOI: doi:10.1038/s41422-020-00444-y ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Fab p17 heavy chain (13 kDa, Protein from Homo sapiens)
- Fab p17 light chain (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab p17 (Complex from Homo sapiens)
- Complex of sars-cov-2 spike protein and fab p17 with one rbd in closed state and two rbds in open state. (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7cwm
Q-score: 0.277
Yao H, Sun Y, Deng YQ, Wang N, Tan Y, Zhang NN, Li XF, Kong C, Xu YP, Chen Q, Cao TS, Zhao H, Yan X, Cao L, Lv Z, Zhu D, Feng R, Wu N, Zhang W, Hu Y, Chen K, Zhang RR, Lv Q, Sun S, Zhou Y, Yan R, Yang G, Sun X, Liu C, Lu X, Cheng L, Qiu H, Huang XY, Weng T, Shi D, Jiang W, Shao J, Wang L, Zhang J, Jiang T, Lang G, Qin CF, Li L, Wang X
Cell Res (2021) 31 pp. 25-36 [ Pubmed: 33262452 DOI: doi:10.1038/s41422-020-00444-y ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- The complex of sars-cov-2 spike protein and p17 with one rbd open and two rbds closed (Complex)
- P17 (Complex from Homo sapiens)
- Sars-cov-2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- P17 heavy chain (13 kDa, Protein from Homo sapiens)
- P17 light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
P17-H014 Fab cocktail in complex with SARS-CoV-2 spike protein
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7cwn
Q-score: 0.224
Yao H, Sun Y, Deng YQ, Wang N, Tan Y, Zhang NN, Li XF, Kong C, Xu YP, Chen Q, Cao TS, Zhao H, Yan X, Cao L, Lv Z, Zhu D, Feng R, Wu N, Zhang W, Hu Y, Chen K, Zhang RR, Lv Q, Sun S, Zhou Y, Yan R, Yang G, Sun X, Liu C, Lu X, Cheng L, Qiu H, Huang XY, Weng T, Shi D, Jiang W, Shao J, Wang L, Zhang J, Jiang T, Lang G, Qin CF, Li L, Wang X
Cell Res (2021) 31 pp. 25-36 [ Pubmed: 33262452 DOI: doi:10.1038/s41422-020-00444-y ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- H014 and p17 fab cocktail in complex with sars-cov-2 spike protein (Complex)
- H014 fab (Complex from Homo sapiens)
- Sars-cov-2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- P17 fab (Complex from Homo sapiens)
- Heavy chain of h014 fab (22 kDa, Protein from Homo sapiens)
- Light chain of h014 fab (22 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Heavy chain of p17 fab (22 kDa, Protein from Homo sapiens)
- Light chain of p17 fab (22 kDa, Protein from Homo sapiens)
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6wjd
Q-score: 0.23
Chen X, Dorris Z, Shi D, Huang RK, Khant H, Fox T, de Val N, Williams D, Zhang P, Walters KJ
Structure (2020) 28 pp. 1206-1217.e4 [ Pubmed: 32783951 DOI: doi:10.1016/j.str.2020.07.011 ]
- 26s proteasome regulatory subunit 10b (45 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-7 (27 kDa, Protein from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 26s proteasome regulatory subunit 7 (48 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-4 (29 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-7 (29 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-2 (25 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 26s proteasome non-atpase regulatory subunit 12 (52 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 11 (47 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 7 (37 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 8 (39 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 6a (49 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 13 (42 kDa, Protein from Homo sapiens)
- 26s proteasome complex subunit sem1 (8 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 4 (49 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-4 (29 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-6 (27 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-2 (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Proteasome subunit beta type-5 (28 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-3 (28 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-3 (22 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-5 (26 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-6 (25 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 14 (34 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 6 (45 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 8 (44 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 4 (40 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 1 (105 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-1 (30 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-1 (26 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 6b (47 kDa, Protein from Homo sapiens)
- Human 26s proteasome with non-cleavable m1-linked hexaubiquitin and e3 ubiquitin ligase e6ap/ube3a (Complex from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 3 (61 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 2 (100 kDa, Protein from Homo sapiens)
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 6wjn
Q-score: 0.174
Chen X, Dorris Z, Shi D, Huang RK, Khant H, Fox T, de Val N, Williams D, Zhang P, Walters KJ
Structure (2020) 28 pp. 1206-1217.e4 [ Pubmed: 32783951 DOI: doi:10.1016/j.str.2020.07.011 ]
- Proteasome subunit alpha type-5 (25 kDa, Protein from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- 26s proteasome non-atpase regulatory subunit 7 (32 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-4 (28 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 8 (30 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-2 (25 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-6 (20 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 4 (20 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 12 (52 kDa, Protein from Homo sapiens)
- Sd-like state of human 26s proteasome with non-cleavable m1-linked hexaubiquitin and e3 ubiquitin ligase e6ap/ube3a (Complex from Homo sapiens)
- Proteasome subunit alpha type-6 (26 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 6b (43 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-7 (27 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 14 (32 kDa, Protein from Homo sapiens)
- 26s proteasome complex subunit sem1 (8 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-7 (23 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 6a (44 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 4 (43 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 11 (42 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-1 (26 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 10b (42 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 3 (54 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 26s proteasome non-atpase regulatory subunit 6 (44 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-1 (23 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-2 (22 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 1 (101 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-3 (22 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 13 (42 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 7 (44 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-5 (22 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-3 (27 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-4 (23 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 8 (44 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 2 (100 kDa, Protein from Homo sapiens)
1.01 A MicroED structure of GSNQNNF at 0.27 e- / A^2
Resolution: 1.01 Å
EM Method: Electron Crystallography
Fitted PDBs: 6clc
Q-score: 0.958
Hattne J, Shi D, Glynn C, Zee CT, Gallagher-Jones M, Martynowycz MW, Rodriguez JA, Gonen T
Structure (2018) 26 pp. 759-766.e4 [ DOI: doi:10.1016/j.str.2018.03.021 Pubmed: 29706530 ]
- Synthetic proto-filament (899 Da, Complex)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Gsnqnnf (779 Da, Protein from synthetic construct)
- Acetate ion (59 Da, Ligand)