Inactive Mu-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound#020_E1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9mqi
Q-score: 0.352
Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbolle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.09.632033 Pubmed: 39868130 ]
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Mu-type opioid receptor (46 kDa, Protein from Homo sapiens)
- Nabfab light chain (23 kDa, Protein from synthetic construct)
- Nabfab heavy chain (25 kDa, Protein from synthetic construct)
- Methyl (1s,3r,4s,6s,8m)-2-[(1-ethyl-1h-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)-3,4-dimethyl-2-azabicyclo[2.2.2]oct-7-ene-6-carboxylate (395 Da, Ligand)
- Human mu-opioid receptor (46 MDa, Complex from Homo sapiens)
Inactive Kappa-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound #020_E1
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 9mqk
Q-score: 0.466
Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbolle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.09.632033 Pubmed: 39868130 ]
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Nabfab light chain (23 kDa, Protein from synthetic construct)
- Nabfab heavy chain (25 kDa, Protein from synthetic construct)
- Methyl (1s,3r,4s,6s,8m)-2-[(1-ethyl-1h-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)-3,4-dimethyl-2-azabicyclo[2.2.2]oct-7-ene-6-carboxylate (395 Da, Ligand)
- Human kappa-opioid receptor (46 MDa, Complex from Homo sapiens)
- Kappa-opioid receptor (43 kDa, Protein from Homo sapiens)
Integrin alpha-5 beta-1 in complex with BIIG2 Fab
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9b9j
Q-score: 0.589
Nguyen A, Heim JB, Cordara G, Chan MC, Johannesen H, Charlesworth C, Li M, Azumaya CM, Madden B, Krengel U, Meves A, Campbell MG
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.08.631572 Pubmed: 39829743 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Biig2 fab light chain (23 kDa, Protein from Rattus norvegicus)
- Calcium ion (40 Da, Ligand)
- Protein complex of integrin alpha-5 beta-1 with biig2 fab (Complex from Homo sapiens)
- Integrin alpha-5 light chain (108 kDa, Protein from Homo sapiens)
- Biig2 fab heavy chain (23 kDa, Protein from Rattus norvegicus)
- Integrin beta-1 (80 kDa, Protein from Homo sapiens)
Integrin alpha-5 beta-1 in complex with MINT1526A Fab
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b9k
Q-score: 0.547
Nguyen A, Heim JB, Cordara G, Chan MC, Johannesen H, Charlesworth C, Li M, Azumaya CM, Madden B, Krengel U, Meves A, Campbell MG
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.08.631572 Pubmed: 39829743 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Protein complex of integrin alpha-5 beta-1 with mint1526a fab (Complex from Homo sapiens)
- Integrin alpha-5 light chain (108 kDa, Protein from Homo sapiens)
- Mint1526a fab heavy chain (13 kDa, Protein from unidentified)
- Mint1526a fab light chain (11 kDa, Protein from unidentified)
- Integrin beta-1 (80 kDa, Protein from Homo sapiens)
G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 9cq4
Q-score: 0.464
Hoque M, Grigg JB, Ramlall T, Jones J, McGoldrick LL, Lin JC, Olson WC, Smith E, Franklin MC, Zhang T, Saotome K
Nat Commun (2025) 16 pp. 318-318 [ DOI: doi:10.1038/s41467-024-55467-5 Pubmed: 39747888 ]
- G115 tcr delta chain (31 kDa, Protein from Homo sapiens)
- G115 tcr gamma chain (33 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 zeta chain (19 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- G115 gamma delta tcr/cd3 complex bound by okt3 fab (Complex from Homo sapiens)
- Okt3 fab heavy chain (25 kDa, Protein from Mus musculus)
- T-cell surface glycoprotein cd3 delta chain (19 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 gamma chain (20 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- T-cell surface glycoprotein cd3 epsilon chain (23 kDa, Protein from Homo sapiens)
- Okt3 fab light chain (23 kDa, Protein from Mus musculus)
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)
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)
Composite cryoEM map of CD20 in complex with wild type Rituximab Fab
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8vgn
Q-score: 0.549
Kung JE, Johnson MC, Jao CC, Arthur CP, Tegunov D, Rohou A, Sudhamsu J
bioRxiv (2024) [ DOI: doi:10.1101/2024.05.10.593593 Pubmed: 38798381 ]
- Rituximab fab heavy chain (24 kDa, Protein from Homo sapiens)
- Cd20 (Complex from Homo sapiens)
- Cd20 in complex with rituximab fab (Complex)
- Rituximab fab (Complex from Homo sapiens)
- B-lymphocyte antigen cd20 (31 kDa, Protein from Homo sapiens)
- Rituximab fab light chain (23 kDa, Protein from Homo sapiens)