Kawamoto A, Vizarraga D, Marcos-Silva M, Martin J, Makino F, Miyata T, Roel J, Marcos E, Aparicio D, Fita I, Miyata M, Pinyol J, Namba K, Kenri T
To Be Published
- Water (18 Da, Ligand)
- Anti-adhesive fab fragment (Complex from Mus musculus)
- Adhesin p1 (158 kDa, Protein from Mycoplasmoides pneumoniae M129)
- Heavy chain fab (23 kDa, Protein from Mus musculus)
- Mycoplasma pneumoniae adhesin p1 complexed with the anti-adhesive fab fragment. (200 kDa, Complex)
- Light chain fab (24 kDa, Protein from Mus musculus)
- Adhesin p1 (Complex from Mycoplasmoides pneumoniae M129)
Dimeric 9C2 gamma delta TCR bound by Fab 3
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9cql
Q-score: 0.467
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 [ Pubmed: 39747888 DOI: doi:10.1038/s41467-024-55467-5 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- G115 gamma delta tcr/cd3 complex bound by okt3 fab (Complex from Homo sapiens)
- Anti tcr variable delta 1 fab heavy chain fab 3 (24 kDa, Protein from Mus musculus)
- Beta-d-mannopyranose (180 Da, Ligand)
- 9c2 tcr gamma chain (33 kDa, Protein from Homo sapiens)
- 9c2 tcr delta chain (31 kDa, Protein from Homo sapiens)
- Anti tcr variable delta 1 fab light chain fab 3 (24 kDa, Protein from Mus musculus)
Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8p12
Q-score: 0.304
Pamula F, Tejero O, Muehle J, Thoma R, Schertler GFX, Marino J, Tsai C-J
To Be Published
- Guanine nucleotide-binding protein g(t) subunit gamma-t1 (8 kDa, Protein from Bos taurus)
- Rhodopsin (39 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 and guanine nucleotide-binding protein g(t) subunit gamma-t1 (Complex from Bos taurus)
- Immunoglobin g heavy chain fab fragment (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (43 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Bos taurus)
- Rhodopsin-gi-fab13 complex (170 kDa, Complex)
- Immunoglobin g light chain (26 kDa, Protein from Mus musculus)
- Immunoglobin g light chain and immunoglobin g heavy chain fab fragment (Complex from Mus musculus)
- Rhodopsin (Complex from Bos taurus)
Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 1
Resolution: 5.2 Å
EM Method: Single-particle
Fitted PDBs: 8p13
Q-score: 0.198
Pamula F, Tejero O, Muehle J, Thoma R, Schertler GFX, Marino J, Tsai C-J
To Be Published
- Rhodopsin-gi-scfv16-fab79 complex (195 kDa, Complex)
- Guanine nucleotide-binding protein g(t) subunit gamma-t1 (8 kDa, Protein from Bos taurus)
- Rhodopsin (39 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 and guanine nucleotide-binding protein g(t) subunit gamma-t1 (Complex from Bos taurus)
- Single-chain fv 16 (27 kDa, Protein from Mus musculus)
- Immunoglobin g heavy chain fab fragment (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (43 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Bos taurus)
- Immunoglobin g light chain (26 kDa, Protein from Mus musculus)
- Immunoglobin g heavy chain fab fragment and immunoglobin g light chain (Complex from Mus musculus)
- Single-chain fv 16 (Complex from Mus musculus)
- Rhodopsin (Complex from Bos taurus)
Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 2
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 8p15
Q-score: 0.207
Pamula F, Tejero O, Muehle J, Thoma R, Schertler GFX, Marino J, Tsai C-J
To Be Published
- Rhodopsin-gi-scfv16-fab79 complex (195 kDa, Complex)
- Guanine nucleotide-binding protein g(t) subunit gamma-t1 (8 kDa, Protein from Bos taurus)
- Rhodopsin (39 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 and guanine nucleotide-binding protein g(t) subunit gamma-t1 (Complex from Bos taurus)
- Single-chain fv scfv16 (Complex from Mus musculus)
- Immunoglobin g heavy chain fab fragment (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (43 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Bos taurus)
- Immunoglobin g light chain (26 kDa, Protein from Mus musculus)
- Single-chain fv scfv16 (27 kDa, Protein from Mus musculus)
- Immunoglobin g heavy chain fab fragment and immunoglobin g light chain (Complex from Mus musculus)
- Rhodopsin (Complex from Bos taurus)
Zhu J, Liang M, Sun K, Wei Y, Guo R, Zhang L, Shi J, Ma D, Hu Q, Huang G, Lu P
Nature (2025) [ Pubmed: 39972138 DOI: doi:10.1038/s41586-025-08598-8 ]
- De novo design of hbc599 membrane protein binder (Complex from artificial sequences)
- Hbc599 membrane protein binder (33 kDa, Protein from artificial sequences)
- Heavy chain, fab fragment (24 kDa, Protein from Homo sapiens)
- Light chain, fab fragment (23 kDa, Protein from Homo sapiens)
- 4-[(z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile (359 Da, Ligand)
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 8tqi
Q-score: 0.499
Suryadevara N, Otrelo-Cardoso AR, Kose N, Hu YX, Binshtein E, Wolters RM, Greninger AL, Handal LS, Carnahan RH, Moscona A, Jardetzky TS, Crowe Jr JE
Nat Microbiol (2024) 9 pp. 2128-2143 [ Pubmed: 38858594 DOI: doi:10.1038/s41564-024-01722-w ]
- Light chain fab rpiv3-23 (23 kDa, Protein from Homo sapiens)
- Hemagglutinin-neuraminidase glycoprotein (Complex from Human respirovirus 3)
- Recombinant rpiv3-28 fab (Complex from Homo sapiens)
- Heavy chain fab rpiv3-28 (23 kDa, Protein from Homo sapiens)
- Light chain fab rpiv3-28 (23 kDa, Protein from Homo sapiens)
- Heavy chain fab rpiv3-23 (24 kDa, Protein from Homo sapiens)
- Hemagglutinin-neuraminidase (50 kDa, Protein from Human respirovirus 3)
- Hpiv3 hn in complex with rpiv3-23 and rpiv3-28 fabs (Complex from Human respirovirus 3)
- Recombinant rpiv3-23 fab (Complex from Homo sapiens)
Human parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8tqk
Q-score: 0.451
Suryadevara N, Otrelo-Cardoso AR, Kose N, Hu YX, Binshtein E, Wolters RM, Greninger AL, Handal LS, Carnahan RH, Moscona A, Jardetzky TS, Crowe Jr JE
Nat Microbiol (2024) 9 pp. 2128-2143 [ Pubmed: 38858594 DOI: doi:10.1038/s41564-024-01722-w ]
- Light chain fab rpiv3-28 (23 kDa, Protein from Homo sapiens)
- Fusion glycoprotein f0 (57 kDa, Protein from Human respirovirus 3)
- Hpiv3 prefusion f trimer in complex with rpiv3-18 fab (Complex from Human respirovirus 3)
- Rpiv3-18 heavy chain (Complex from Homo sapiens)
- Heavy chain fab rpiv3-18 (23 kDa, Protein from Homo sapiens)
- Fusion glycoprotein f0 (Complex from Human respirovirus 3)
- Rpiv3-18 light chain (Complex from Homo sapiens)
SARS-CoV-2 S protein bound to human neutralising antibody UZGENT_G5
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qpr
Q-score: 0.469
Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L
Ebiomedicine (2024) 100 pp. 104960-104960 [ DOI: doi:10.1016/j.ebiom.2023.104960 Pubmed: 38232633 ]
- Complex of sars-cov2 s protein (wuhan) and fab fragment of neutralising human antibody uzgent_g5 (Complex)
- Igg light chain - fab (22 kDa, Protein from Homo sapiens)
- Sars-cov2 s protein with fibritin (trimerization) tag (Complex from Severe acute respiratory syndrome coronavirus 2)
- Igg heavy chain - fab (24 kDa, Protein from Homo sapiens)
- Fab fragment of neutralising human antibody uzgent_g5 (Complex from Homo sapiens)
- Spike glycoprotein,fibritin (142 kDa, Protein from Tequatrovirus T4)
SARS-CoV-2 S protein bound to neutralising antibody UZGENT_A3
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qq0
Q-score: 0.534
Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L
Ebiomedicine (2024) 100 pp. 104960-104960 [ DOI: doi:10.1016/j.ebiom.2023.104960 Pubmed: 38232633 ]
- Igg light chain - fab (22 kDa, Protein from Homo sapiens)
- Igg heavy chain - fab (24 kDa, Protein from Homo sapiens)
- Sars-cov2 s protein with fibritin (trimerization) tag (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- Fab fragment of neutralising human antibody uzgent_a3 (Complex from Homo sapiens)
- Complex of sars-cov2 s protein (wuhan) and fab fragment of neutralising human antibody uzgent_a3 (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)