SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 8c2r
Q-score: 0.436
Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hallberg BM
Cell Rep Med (2024) 5 pp. 101577-101577 [ Pubmed: 38761799 DOI: doi:10.1016/j.xcrm.2024.101577 ]
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (fab) (Complex from Enterobacteria phage T4)
- Sars-cov2 omicron ba.1 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Cab-a17 antibody (hc) (22 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov2 omicron ba.1 spike in complex with cab-a17 antibody (95 kDa, Complex)
- Cab-a17 antibody (lc) (23 kDa, Protein from Homo sapiens)
Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with 2130-1-0114-112
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ekd
Q-score: 0.433
Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Dadonaite B, Petersen BK, Engdahl TB, Chen E, Handal LS, Hall L, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JK, Rubinfeld B, Saada EA, Weisenberger T, Lee TH, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Earnhart CG, Hopkins S, Bates TW, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Bloom JD, Diamond MS, Crowe Jr JE, Carnahan RH, Faissol DM
Nature (2024) 629 pp. 878-885 [ DOI: doi:10.1038/s41586-024-07385-1 Pubmed: 38720086 ]
- Fab llnl-199 hc (14 kDa, Protein from Homo sapiens)
- Fab llnl-199 (Complex from Homo sapiens)
- Sars cov2 omicron ba.2 rbd complex with fab llnl-199 (Complex)
- Sars cov2 omicron ba.2 rbd (Complex from Severe acute respiratory syndrome coronavirus)
- Fab llnl-199 lc (12 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s2' (20 kDa, Protein from Severe acute respiratory syndrome coronavirus)
96-nm repeat unit of doublet microtubules from Chlamydomonas reinhardtii flagella
Walton T, Gui M, Velkova S, Fassad MR, Hirst RA, Haarman E, O'Callaghan C, Bottier M, Burgoyne T, Mitchison HM, Brown A
Nature (2023) 618 pp. 625-633 [ Pubmed: 37258679 DOI: doi:10.1038/s41586-023-06140-2 ]
- Flagellar associated protein (16 kDa, Protein from Chlamydomonas reinhardtii)
- Fap44 (222 kDa, Protein from Chlamydomonas reinhardtii)
- Fap143 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein-1-beta heavy chain, flagellar inner arm i1 complex (511 kDa, Protein from Chlamydomonas reinhardtii)
- Fap306 (20 kDa, Protein from Chlamydomonas reinhardtii)
- Fap34 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 77 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 14 kda light chain, flagellar outer arm (14 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (177 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spike protein 8 (40 kDa, Protein from Chlamydomonas reinhardtii)
- Fap21 (49 kDa, Protein from Chlamydomonas reinhardtii)
- Coiled-coil protein associated with protofilament ribbons (42 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 45 (59 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain roadblock lc7b (11 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm-docking complex protein dc3 (21 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown (2 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (25 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 100 (65 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 16 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Nucleoside diphosphate kinase 6 (61 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 299 (27 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar-associated protein 59 (105 kDa, Protein from Chlamydomonas reinhardtii)
- Actin (41 kDa, Protein from Chlamydomonas reinhardtii)
- Ic97/casc1 n-terminal domain-containing protein (81 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (35 kDa, Protein from Chlamydomonas reinhardtii)
- Protein flattop homolog (15 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (15 kDa, Protein from Chlamydomonas reinhardtii)
- Dhc_n2 domain-containing protein (465 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (48 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 5 (55 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown (6 kDa, Protein from Chlamydomonas reinhardtii)
- 96-nm repeat unit of doublet microtubules from the flagella of chlamydomonas reinhardtii (Complex from Chlamydomonas reinhardtii)
- Flagellar associated protein (267 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dynein 18 kda light chain, flagellar outer arm (17 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (27 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin alpha (49 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar-associated protein 172 (101 kDa, Protein from Chlamydomonas reinhardtii)
- Wd_repeats_region domain-containing protein (146 kDa, Protein from Chlamydomonas reinhardtii)
- Fap43 (199 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (22 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein axonemal light chain 1 (22 kDa, Protein from Chlamydomonas reinhardtii)
- Pacrg (34 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex subunit 6 (28 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 14 (40 kDa, Protein from Chlamydomonas reinhardtii)
- Fap1 (21 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (15 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (32 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm-docking complex subunit 1 (83 kDa, Protein from Chlamydomonas reinhardtii)
- Magnesium ion (24 Da, Ligand)
- Radial spoke protein 9 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 4 (49 kDa, Protein from Chlamydomonas reinhardtii)
- Aaa+ atpase domain-containing protein (470 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain tctex1 (12 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 8 kda light chain, flagellar outer arm (10 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein, 78 kda intermediate chain, flagellar outer arm (76 kDa, Protein from Chlamydomonas reinhardtii)
- Subunit of axonemal inner dynein (40 kDa, Protein from Chlamydomonas reinhardtii)
- Fap210 (53 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 10 (23 kDa, Protein from Chlamydomonas reinhardtii)
- Atpase aaa-type core domain-containing protein (94 kDa, Protein from Chlamydomonas reinhardtii)
- Peptidyl-prolyl cis-trans isomerase (19 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 1 (87 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 7 (54 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (27 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (26 kDa, Protein from Chlamydomonas reinhardtii)
- Fap166 (23 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 16 kda light chain, flagellar outer arm (17 kDa, Protein from Chlamydomonas reinhardtii)
- Drc5 (43 kDa, Protein from Chlamydomonas reinhardtii)
- Fap251 (97 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar outer dynein arm light chain 2 (15 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 73 (35 kDa, Protein from Chlamydomonas reinhardtii)
- Fap207 (28 kDa, Protein from Chlamydomonas reinhardtii)
- 28 kda inner dynein arm light chain, axonemal (28 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 11 kda light chain, flagellar outer arm (13 kDa, Protein from Chlamydomonas reinhardtii)
- Inner-arm dynein f/i1 light chain (26 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 6 (48 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (43 kDa, Protein from Chlamydomonas reinhardtii)
- Fap385 (8 kDa, Protein from Chlamydomonas reinhardtii)
- Aaa+ atpase domain-containing protein (523 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (25 kDa, Protein from Chlamydomonas reinhardtii)
- Axonemal inner arm i1 intermediate chain dynein ic138 (111 kDa, Protein from Chlamydomonas reinhardtii)
- Protofilament ribbon protein of flagellar microtubules (72 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 11 (21 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain 10 (12 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 3 (56 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain roadblock lc7a (11 kDa, Protein from Chlamydomonas reinhardtii)
- Inner arm dynein light chain (13 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 20 (22 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin beta (49 kDa, Protein from Chlamydomonas reinhardtii)
- Aaa+ atpase domain-containing protein (478 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (42 kDa, Protein from Chlamydomonas reinhardtii)
- Ic140 (109 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm protein 1 (62 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex subunit 4 (55 kDa, Protein from Chlamydomonas reinhardtii)
- Cfap91 domain-containing protein (134 kDa, Protein from Chlamydomonas reinhardtii)
- Heavy chain alpha (504 kDa, Protein from Chlamydomonas reinhardtii)
- Axonemal inner arm dynein i1/f subunit (31 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke protein 15 (35 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 2 (77 kDa, Protein from Chlamydomonas reinhardtii)
- Fap129 (51 kDa, Protein from Chlamydomonas reinhardtii)
- Duf4201 domain-containing protein (45 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex protein 8 (18 kDa, Protein from Chlamydomonas reinhardtii)
- Fap253 (75 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex protein 1 (79 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar outer dynein arm heavy chain beta (520 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex subunit 2 (64 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (12 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 53 (56 kDa, Protein from Chlamydomonas reinhardtii)
- Caltractin (19 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Dynein regulatory complex subunit 3 (60 kDa, Protein from Chlamydomonas reinhardtii)
- Subunit of axonemal inner dynein (46 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b5 heme-binding domain-containing protein (26 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar associated protein (53 kDa, Protein from Chlamydomonas reinhardtii)
- Nucleoside diphosphate kinase (41 kDa, Protein from Chlamydomonas reinhardtii)
- Aaa+ atpase domain-containing protein (468 kDa, Protein from Chlamydomonas reinhardtii)
- Fap52 (68 kDa, Protein from Chlamydomonas reinhardtii)
- Fap339 (10 kDa, Protein from Chlamydomonas reinhardtii)
- Dhc2 (467 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein gamma chain, flagellar outer arm (513 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 61 (121 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain 9 (12 kDa, Protein from Chlamydomonas reinhardtii)
- Aaa+ atpase domain-containing protein (464 kDa, Protein from Chlamydomonas reinhardtii)
- Duf4201 domain-containing protein (55 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex protein 10 (40 kDa, Protein from Chlamydomonas reinhardtii)
- Calmodulin (18 kDa, Protein from Chlamydomonas reinhardtii)
- Meiosis-specific nuclear structural protein 1 (59 kDa, Protein from Chlamydomonas reinhardtii)
- Cilia- and flagella-associated protein 58 (102 kDa, Protein from Chlamydomonas reinhardtii)
- Wd_repeats_region domain-containing protein (63 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein regulatory complex protein 9 (46 kDa, Protein from Chlamydomonas reinhardtii)
Tetanus neurotoxin HC domain in complex with TT104-Fab1
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7oh1
Q-score: 0.039
Pirazzini M, Grinzato A, Corti D, Barbieri S, Leka O, Vallese F, Tonellato M, Silacci-Fregni C, Piccoli L, Kandiah E, Schiavo G, Zanotti G, Lanzavecchia A, Montecucco C
J Clin Inv (2021) 131 [ DOI: doi:10.1172/JCI151676 Pubmed: 34618682 ]
- Tetanus neurotoxin lc-hn domain in complex with tt110-fab1 (Complex)
- Tetanus toxin (99 kDa, Protein from Clostridium tetani)
- Fab tt110 (24 kDa, Protein from Homo sapiens)
- Fab tt110 (Complex from Homo sapiens)
- Fab tt110 (23 kDa, Protein from Homo sapiens)
- Tetanus toxin (Complex from Clostridium tetani)
ASCT2 in the presence of the inhibitor Lc-BPE in the outward-open conformation.
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 7bcq
Q-score: 0.427
Garibsingh RA, Ndaru E, Garaeva AA, Shi Y, Zielewicz L, Zakrepine P, Bonomi M, Slotboom DJ, Paulino C, Grewer C, Schlessinger A
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2104093118 Pubmed: 34507995 ]
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 7php
Q-score: 0.505
Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP
PNAS (2021) 118 [ Pubmed: 34782475 DOI: doi:10.1073/pnas.2115435118 ]
- Water (18 Da, Ligand)
- Complex of vibrio cholerae mate transporter norm, chimeric nanobody norm-nb17_4, nabfab, and anti-fab nanobody (Complex from Vibrio cholerae RC385)
- Nabfab lc (23 kDa, Protein from synthetic construct)
- Norm-nb17_4 (14 kDa, Protein from synthetic construct)
- Anti-fab nanobody (13 kDa, Protein from Lama glama)
- Nabfab hc (25 kDa, Protein from synthetic construct)
- Multidrug resistance protein norm (52 kDa, Protein from Vibrio cholerae RC385)
Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP
PNAS (2021) 118 [ Pubmed: 34782475 DOI: doi:10.1073/pnas.2115435118 ]
- Anti-fab nanobody (Complex)
- Complex of vibrio cholerae mate transporter norm, chimeric nanobody norm-nb17_4, nabfab, and anti-fab nanobody (Complex from Vibrio cholerae RC385)
- Nabfab hc (Complex from synthetic construct)
- Nabfab lc (Complex from synthetic construct)
- Multidrug resistance protein norm (Complex from synthetic construct)
- Norm-nb17_4 (Complex from Lama glama)
Resolution: 8.45 Å
EM Method: Single-particle
Fitted PDBs: 7phq
Q-score: 0.111
Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP
PNAS (2021) 118 [ Pubmed: 34782475 DOI: doi:10.1073/pnas.2115435118 ]
- Water (18 Da, Ligand)
- Complex of staphylococcus capitis divalent metal ion transporter (dmt), chimeric nanobody dmtnb16_4, nabfab, and anti-fab nanobody (Complex from synthetic construct)
- Dmt-nb16_4 (14 kDa, Protein from synthetic construct)
- Nabfab lc (23 kDa, Protein from synthetic construct)
- Divalent metal cation transporter mnth (47 kDa, Protein from Staphylococcus capitis)
- Anti-fab nanobody (13 kDa, Protein from Lama glama)
- Nabfab hc (25 kDa, Protein from synthetic construct)
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 7pij
Q-score: 0.422
Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP
PNAS (2021) 118 [ Pubmed: 34782475 DOI: doi:10.1073/pnas.2115435118 ]
- Water (18 Da, Ligand)
- Complex of staphylococcus capitis divalent metal ion transporter (dmt), chimeric nanobody dmtnb16_4, nabfab, and anti-fab nanobody (Complex from synthetic construct)
- Nabfab lc (23 kDa, Protein from synthetic construct)
- Divalent metal cation transporter mnth (47 kDa, Protein from Staphylococcus capitis)
- Anti-fab nanobody (13 kDa, Protein from Lama glama)
- Nabfab hc (25 kDa, Protein from synthetic construct)
- Dmtnb16_4 (14 kDa, Protein from synthetic construct)
BDBV-289 bound to EBOV GPdMuc Makona
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7kej
Q-score: 0.451
Murin CD, Gilchuk P, Ilinykh PA, Huang K, Kuzmina N, Shen X, Bruhn JF, Bryan AL, Davidson E, Doranz BJ, Williamson LE, Copps J, Alkutkar T, Flyak AI, Bukreyev A, Crowe Jr JE, Ward AB
Cell Rep (2021) 35 pp. 108984-108984 [ Pubmed: 33852862 DOI: doi:10.1016/j.celrep.2021.108984 ]
- Virion spike glycoprotein (22 kDa, Protein from Zaire ebolavirus)
- Antibody fab light chain (lc) bdbv-289 (24 kDa, Protein from Homo sapiens)
- Complex of ebola virus gp (mucin-deleted makona strain) bound to bdbv-289 fab (Complex from Homo sapiens)
- Antibody fab heavy chain (hc) bdbv-289 (26 kDa, Protein from Homo sapiens)
- Virion spike glycoprotein (34 kDa, Protein from Ebola virus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)