Cryo-EM structure of neutralizing antibody 8G3 in complex with BA.1 RBD
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9js4
Q-score: 0.434
Liao Y, Ma H, Wang Z, Wang S, He Y, Chang Y, Zong H, Tang H, Wang L, Ke Y, Cai H, Li P, Tang J, Chen H, Drelich A, Peng BH, Hsu J, Tat V, Tseng CK, Song J, Yuan Y, Wu M, Liu J, Yue Y, Zhang X, Wang Z, Yang L, Li J, Ni X, Li H, Xiang Y, Bian Y, Zhang B, Yin H, Dimitrov DS, Gilly J, Han L, Jiang H, Xie Y, Zhu J
PNAS (2025) 122 pp. e2406659122-e2406659122 [ Pubmed: 39908098 DOI: doi:10.1073/pnas.2406659122 ]
- Cryo-em structure of neutralizing antibody 8g3 in complex with ba.1 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Heavy chain of 8g3 (23 kDa, Protein from Homo heidelbergensis)
- Light chain of 8g3 (23 kDa, Protein from Homo sapiens)
cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9dqd
Q-score: 0.467
Lejava A, Miseo GA, Phan T, Zhu J, Powers HL, Li J, Mortensen DS, Zapf CW, Khambatta G, Buenviaje J, Holmberg-Douglas N
Acs Med.Chem.Lett. (2025) 16 pp. 89-95 [ Pubmed: 39811117 DOI: doi:10.1021/acsmedchemlett.4c00462 ]
- Zinc ion (65 Da, Ligand)
- (3r)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1h-indazol-3-yl}piperidine-2,6-dione (341 Da, Ligand)
- Crebn-ddb1 plus a non-traditional crbn binder (Complex from Homo sapiens)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- Protein cereblon (53 kDa, Protein from Homo sapiens)
Cryo-EM structure of IMPDH2 bound to IMP and GAD
Resolution: 1.82 Å
EM Method: Single-particle
Fitted PDBs: 9dmu
Q-score: 0.802
Chen YJ, Iyer SV, Hsieh DC, Li B, Elias HK, Wang T, Li J, Ganbold M, Lien MC, Peng YC, Xie XP, Jayewickreme CD, van den Brink MRM, Brady SF, Lim SK, Parada LF
Nature (2024) 636 pp. 466-473 [ DOI: doi:10.1038/s41586-024-08224-z Pubmed: 39567689 ]
- Potassium ion (39 Da, Ligand)
- [[(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{r},3~{s},4~{r},5~{r})-3,4-bis(oxidanyl)-5-[3-(thiophen-2-ylcarbonylamino)pyridin-1-yl]oxolan-2-yl]methyl hydrogen phosphate (746 Da, Ligand)
- Inosinic acid (348 Da, Ligand)
- Inosine-5'-monophosphate dehydrogenase 2 (56 kDa, Protein from Homo sapiens)
- Ternary complex of impdh2 bound to imp and gad (Complex from Homo sapiens)
- Water (18 Da, Ligand)
The cryo-EM structure of apo KBTBD4
Resolution: 3.83 Å
EM Method: Single-particle
Fitted PDBs: 9dtg
Q-score: 0.432
Yeo MJR, Zhang O, Xie X, Nam E, Payne NC, Gosavi PM, Kwok HS, Iram I, Lee C, Li J, Chen NJ, Nguyen K, Jiang H, Wang ZA, Lee K, Mao H, Harry SA, Barakat IA, Takahashi M, Waterbury AL, Barone M, Mattevi A, Carr SA, Udeshi ND, Bar-Peled L, Cole PA, Mazitschek R, Liau BB, Zheng N
Nature (2025) [ DOI: doi:10.1038/s41586-024-08532-4 Pubmed: 39939761 ]
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9c44
Q-score: 0.535
Liu P, Huang ML, Guo H, McCallum M, Si JY, Chen YM, Wang CL, Yu X, Shi LL, Xiong Q, Ma CB, Bowen JE, Tong F, Liu C, Sun YH, Yang X, Chen J, Guo M, Li J, Corti D, Veesler D, Shi ZL, Yan H
Nature (2024) 635 pp. 978-986 [ Pubmed: 39478224 DOI: doi:10.1038/s41586-024-08121-5 ]
- Sars-cov-2 s bound by s2l20 fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S2l20 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- S2l20 fab heavy chain variable (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9c45
Q-score: 0.552
Liu P, Huang ML, Guo H, McCallum M, Si JY, Chen YM, Wang CL, Yu X, Shi LL, Xiong Q, Ma CB, Bowen JE, Tong F, Liu C, Sun YH, Yang X, Chen J, Guo M, Li J, Corti D, Veesler D, Shi ZL, Yan H
Nature (2024) 635 pp. 978-986 [ Pubmed: 39478224 DOI: doi:10.1038/s41586-024-08121-5 ]
- Sars-cov-2 s bound by s2l20 fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S2l20 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- S2l20 fab heavy chain variable (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of human HCN3 channel with cAMP
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8io0
Q-score: 0.42
Structure of the semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9axl
Q-score: 0.473
Wang L, Wang J, Li J, Walz T, Coller BS
Blood Adv (2024) 8 pp. 4398-4409 [ DOI: doi:10.1182/bloodadvances.2024013177 Pubmed: 38968144 ]
- Calcium ion (40 Da, Ligand)
- Integrin beta-3 (87 kDa, Protein from Homo sapiens)
- Integrin alpha-iib (113 kDa, Protein from Homo sapiens)
- The semi-extended alphaiibbeta3 in complex with r21d10 fab (250 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- R21d10 fab light chain (23 kDa, Protein from Mus musculus)
- R21d10 fab heavy chain (24 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
The map of the bent AlphaIIbBeta3 in complex with R21D10 Fab
Wang L, Wang J, Li J, Walz T, Coller BS
Blood Adv (2024) 8 pp. 4398-4409 [ DOI: doi:10.1182/bloodadvances.2024013177 Pubmed: 38968144 ]
- Integrin alphaiib (Protein from Homo sapiens)
- Alphaiibbeta3 integrin (Complex from Homo sapiens)
- Integrin beta3 (Protein from Homo sapiens)
- R21d10 fab (Complex from Mus musculus)
- R211010 fab light chain (Protein from Mus musculus)
- The semi-extended alphaiibbeta3 in complex with r21d10 fab (250 kDa, Complex)
- R21d10 fab heavy chain (Protein from Mus musculus)
State 2 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5
Zhao X, Qiu T, Huang X, Mao Q, Wang Y, Qiao R, Li J, Mao T, Wang Y, Cun Y, Wang C, Luo C, Yoon C, Wang X, Li C, Cui Y, Zhao C, Li M, Chen Y, Cai G, Geng W, Hu Z, Cao J, Zhang W, Cao Z, Chu H, Sun L, Wang P
Cell Discov (2024) 10 pp. 14-14 [ DOI: doi:10.1038/s41421-024-00648-1 Pubmed: 38320990 ]
- Spike glycoprotein (143 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Pw5-5 heavy chain (49 kDa, Protein from Homo sapiens)
- Pw5-5 light chain (23 kDa, Protein from Homo sapiens)
- Sars spike protein (s) in complex with broadly neutralizing antibody pw5-5 (Complex from Severe acute respiratory syndrome coronavirus 2)