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 ]
- Crebn-ddb1 plus a non-traditional crbn binder (Complex from Homo sapiens)
- (3r)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1h-indazol-3-yl}piperidine-2,6-dione (341 Da, Ligand)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- Protein cereblon (53 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1038/s41586-024-08121-5 Pubmed: 39478224 ]
- Sars-cov-2 s bound by s2l20 fab (Complex from Homo sapiens)
- S2l20 fab heavy chain variable (13 kDa, Protein from Homo sapiens)
- S2l20 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 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 [ Pubmed: 38968144 DOI: doi:10.1182/bloodadvances.2024013177 ]
- Water (18 Da, Ligand)
- R21d10 fab heavy chain (24 kDa, Protein from Mus musculus)
- Calcium ion (40 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- The semi-extended alphaiibbeta3 in complex with r21d10 fab (250 kDa, Complex)
- R21d10 fab light chain (23 kDa, Protein from Mus musculus)
- Integrin alpha-iib (113 kDa, Protein from Homo sapiens)
- Integrin beta-3 (87 kDa, Protein from Homo sapiens)
The Cryo-EM structure of DSR2-Tail tube-NAD+ complex
Wang R, Xu Q, Wu Z, Li J, Guo H, Liao T, Shi Y, Yuan L, Gao H, Yang R, Shi Z, Li F
Nat Commun (2024) 15 pp. 6185-6185 [ DOI: doi:10.1038/s41467-024-50410-0 Pubmed: 39039073 ]
- Tail tube protein (29 kDa, Protein from Bacillus subtilis)
- Dsr2-tail tube protein-nad+ complex (Complex from Bacillus subtilis)
- Sir2-like domain-containing protein (118 kDa, Protein from Bacillus subtilis)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 9ckv
Q-score: 0.482
Wang X, Guillem-Marti J, Kumar S, Lee DS, Cabrerizo-Aguado D, Werther R, Alamo KAE, Zhao YT, Nguyen A, Kopyeva I, Huang B, Li J, Hao Y, Li X, Brizuela-Velasco A, Murray A, Gerben S, Roy A, DeForest CA, Springer T, Ruohola-Baker H, Cooper JA, Campbell MG, Manero JM, Ginebra MP, Baker D
bioRxiv (2024) [ Pubmed: 38979380 DOI: doi:10.1101/2024.06.21.600123 ]
- Calcium ion (40 Da, Ligand)
- Integrin beta-1 (81 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Neonectin (11 kDa, Protein from synthetic construct)
- Manganese (ii) ion (54 Da, Ligand)
- Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein neonectin (Complex from Homo sapiens)
- Integrin alpha-5 (109 kDa, Protein from Homo sapiens)
Resolution: 3.94 Å
EM Method: Single-particle
Fitted PDBs: 8kci
Q-score: 0.356
Huang Y, Xue C, Bu R, Wu C, Li J, Zhang J, Chen J, Shi Z, Chen Y, Wang Y, Liu Z
Nat Commun (2024) 15 pp. 4811-4811 [ DOI: doi:10.1038/s41467-024-49204-1 Pubmed: 38844452 ]
- Atp-binding cassette sub-family c member 5 (160 kDa, Protein from Homo sapiens)
- Atp-bound hmrp5 outward-open (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state)
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8xlm
Q-score: 0.382
Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H, Sasaki-Tabata K, Guo Z, Hinay Jr AA, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, Sato K
Microbiol Immunol (2024) 68 pp. 305-330 [ DOI: doi:10.1111/1348-0421.13165 Pubmed: 38961765 ]
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 eg.5.1 spike glycoprotein in complex with ace2 (90 kDa, Complex)
- Sars-cov-2 eg.5.1 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (Complex from Homo sapiens)
Structure of the SARS-CoV-2 EG.5.1 spike RBD in complex with ACE2
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 8xln
Q-score: 0.447
Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H, Sasaki-Tabata K, Guo Z, Hinay Jr AA, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, Sato K
Microbiol Immunol (2024) 68 pp. 305-330 [ DOI: doi:10.1111/1348-0421.13165 Pubmed: 38961765 ]
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 eg.5.1 spike glycoprotein in complex with ace2 (90 kDa, Complex)
- Sars-cov-2 eg.5.1 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (Complex from Homo sapiens)
Cryo-EM structure of adenosine receptor A3AR bound to CF101
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8x16
Q-score: 0.31
Cai H, Guo S, Xu Y, Sun J, Li J, Xia Z, Jiang Y, Xie X, Xu HE
Nat Commun (2024) 15 pp. 3252-3252 [ DOI: doi:10.1038/s41467-024-47207-6 Pubmed: 38627384 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- A3ar (Complex from Homo sapiens)
- Piclidenoson (510 Da, Ligand)
- G protein (Complex from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Cryo-em structure of adenosine receptor a3ar bound to cf101 (160 kDa, Complex)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Bos taurus)
- G protein (Complex from Bos taurus)
- Scfv16 (26 kDa, Protein from Mus musculus)
- Adenosine receptor a3 (36 kDa, Protein from Homo sapiens)