Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with LLNL-199
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 [ Pubmed: 38720086 DOI: doi:10.1038/s41586-024-07385-1 ]
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 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab llnl-199 hc (14 kDa, Protein from Homo sapiens)
- Fab llnl-199 lc (12 kDa, Protein from Homo sapiens)
- Sars cov2 omicron ba.2 rbd (Complex from Severe acute respiratory syndrome coronavirus)
- Sars cov2 omicron ba.2 rbd complex with fab llnl-199 (Complex)
- Fab llnl-199 (Complex from Homo sapiens)
- Spike protein s2' (20 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8fxb
Q-score: 0.469
Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota Jr E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippa P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D
Nature (2023) 621 pp. 592-601 [ Pubmed: 37648855 DOI: doi:10.1038/s41586-023-06487-6 ]
- S309 light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (28 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sars-cov-2 xbb.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 heavy chain (50 kDa, Protein from Homo sapiens)
- Sars-cov-2 xbb.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (74 kDa, Protein from Homo sapiens)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8s9g
Q-score: 0.473
Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota Jr E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippa P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D
Nature (2023) 621 pp. 592-601 [ Pubmed: 37648855 DOI: doi:10.1038/s41586-023-06487-6 ]
- S309 fab heavy chain (24 kDa, Protein from Homo sapiens)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 bn.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (74 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sars-cov-2 bn.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike in complex with AHB2-2GS-SB175 (local refinement of the RBD and AHB2)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7uhb
Q-score: 0.366
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vogeli B, Kruger A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken SE, Ljubetic A, Edman N, Ueda G, Chow CM, Johnson M, Addetia A, Navarro MJ, Panpradist N, Gale Jr M, Freedman BS, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D
Sci Transl Med (2022) 14 pp. eabn1252-eabn1252 [ Pubmed: 35412328 DOI: doi:10.1126/scitranslmed.abn1252 ]
- Multivalent miniprotein inhibitor ahb2-2gs-sb175 (17 kDa, Protein from synthetic construct)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike in complex with ahb2-2gs-sb175 (local refinement of the rbd and ahb2) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ahb2-2gs-sb175 (Complex from Synthetic construct)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
IMM20184 and IMM20253 Fabs in ternary complex with SARS-CoV-2 receptor binding domain
Nikitin PA, DiMuzio JM, Dowling JP, Patel NB, Bingaman-Steele JL, Heimbach BC, Henriquez N, Nicolescu C, Polley A, Sikorski EL, Howanski RJ, Nath M, Shukla H, Scheaffer SM, Finn JP, Liang LF, Smith T, Storm N, McKay LGA, Johnson RI, Malsick LE, Honko AN, Griffiths A, Diamond MS, Sarma P, Geising DH, Morin MJ, Robinson MK
Sci Immunol (2022) 7 pp. eabl9943-eabl9943 [ DOI: doi:10.1126/sciimmunol.abl9943 Pubmed: 35771946 ]
- Imm20184 and imm20253 fabs in ternary complex with rbd of sars-cov-2 (Complex from Severe acute respiratory syndrome coronavirus)
- Imm20253 fab (Complex from Homo sapiens)
- Sars-cov-2 rbd (Complex from Severe acute respiratory syndrome coronavirus)
- Imm20184 fab (Complex from Homo sapiens)