Human leukocyte antigen bound by two alloreactive antibody Fabs
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8t6m
Q-score: 0.498
Killian JT, King RG, Kizziah JL, Fucile CF, Diaz-Avalos R, Qiu S, Silva-Sanchez A, Mousseau BJ, Macon KJ, Callahan AR, Yang G, Hossain ME, Akther J, Houp JA, Rosenblum FD, Porrett PM, Ong SC, Kumar V, Mobley JA, Saphire EO, Kearney JF, Randall TD, Rosenberg AF, Green TJ, Lund FE
To Be Published
- L02/m07/a*01:01 complex (Complex from Homo sapiens)
- Jtk191b_l02_light (23 kDa, Protein from Homo sapiens)
- Jtk191b_m07_light (23 kDa, Protein from Homo sapiens)
- Beta-2-microglobulin (11 kDa, Protein from Homo sapiens)
- Jtk191b_l02_fab (23 kDa, Protein from Homo sapiens)
- Mhc class i antigen (20 kDa, Protein from Homo sapiens)
- Jtk191b_m07_fab (24 kDa, Protein from Homo sapiens)
- Hla_a0101_peptide (1 kDa, Protein from Homo sapiens)
HCMV gH/UL116/UL141 3-mer complex, ectodomain
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 9dix
Q-score: 0.432
Norris MJ, Henderson LA, Siddiquey MNA, Yin J, Yoo K, Brunel S, Saphire EO, Benedict CA, Kamil JP
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.13.617647 Pubmed: 39416215 ]
- Protein ul141 (31 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein h (77 kDa, Protein from Human betaherpesvirus 5)
- Hcmv gh/ul116/ul141 3-mer complex (Complex from Human betaherpesvirus 5)
- Ul116 (35 kDa, Protein from Human betaherpesvirus 5)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Local Cryo-EM structure of HCMV gH/UL116 interaction
Resolution: 5.36 Å
EM Method: Single-particle
Fitted PDBs: 9diy
Q-score: 0.218
Norris MJ, Henderson LA, Siddiquey MNA, Yin J, Yoo K, Brunel S, Saphire EO, Benedict CA, Kamil JP
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.13.617647 Pubmed: 39416215 ]
- Protein ul141 (31 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein h (77 kDa, Protein from Human betaherpesvirus 5)
- Ul116 (35 kDa, Protein from Human betaherpesvirus 5)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Local structure of gh/ul116 interaction (Complex from Human betaherpesvirus 5)
Intracellular cryo-tomography structure of EBOV nucleocapsid at 8.9 Angstrom
Resolution: 8.9 Å
EM Method: Subtomogram averaging
Fitted PDBs: 8usn
Q-score: 0.251
Watanabe R, Zyla D, Parekh D, Hong C, Jones Y, Schendel SL, Wan W, Castillon G, Saphire EO
Cell (2024) 187 pp. 5587-5603.e19 [ Pubmed: 39293445 DOI: doi:10.1016/j.cell.2024.08.044 ]
- Complex (Virus)
- Outer np with vp35 np-binding peptide (Complex from Ebola virus - Mayinga, Zaire, 1976)
- Rna (5'-r(*ap*ap*ap*ap*ap*a)-3') (1 kDa, RNA from Zaire)
- Vp24 second layer of nucleocapsid (Complex from Ebola virus - Mayinga, Zaire, 1976)
- Membrane-associated protein vp24 (28 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
- Nucleoprotein (83 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
- Polymerase cofactor vp35 (37 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
- Np core with rna (Complex from Homo sapiens)
- Vp35 ctd (Complex from Ebola virus - Mayinga, Zaire, 1976)
Structure of EBOV GP lacking the mucin-like domain with 2.1.1D5 scFv and 6D6 scFv bound
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8dpl
Q-score: 0.536
Yu X, Hastie KM, Davis CW, Avalos RD, Williams D, Parekh D, Hui S, Mann C, Hariharan C, Takada A, Ahmed R, Saphire EO
Cell Rep (2023) 42 pp. 113366-113366 [ Pubmed: 37938974 DOI: doi:10.1016/j.celrep.2023.113366 ]
- Structure of ebov gp in complex with 2.1.1d5 scfv and 6d6 scfv (Complex from Ebola virus - Mayinga, Zaire, 1976)
- 2.1.1d5 heavy chain variable domain (13 kDa, Protein from Homo sapiens)
- 2.1.1d5 light chain variable domain (11 kDa, Protein from Homo sapiens)
- Glycoprotein gp2 (15 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glycoprotein gp1 (31 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
- 6d6 single-chain variable fragment (25 kDa, Protein from Mus musculus)
Structure of EBOV GP lacking the mucin-like domain with 9.20.1A2 Fab and 6D6 scFv bound
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8dpm
Q-score: 0.505
Yu X, Hastie KM, Davis CW, Avalos RD, Williams D, Parekh D, Hui S, Mann C, Hariharan C, Takada A, Ahmed R, Saphire EO
Cell Rep (2023) 42 pp. 113366-113366 [ Pubmed: 37938974 DOI: doi:10.1016/j.celrep.2023.113366 ]
- Complex of ebola virus glycoprotein trimer with 1a2 antibody fab and 6d6 antibody scfv (Complex from Ebola virus - Mayinga, Zaire, 1976)
- Glycoprotein gp2 (15 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
- Antibody 6d6 scfv (25 kDa, Protein from Mus musculus)
- Antibody 9.20.1a2 fab light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Antibody 9.20.1a2 fab (Complex from Homo sapiens)
- Antibody 9.20.1a2 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Glycoprotein gp1 (31 kDa, Protein from Ebola virus - Mayinga, Zaire, 1976)
Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8f0g
Q-score: 0.469
Hastie KM, Yu X, Ana-Sosa-Batiz F, Zyla DS, Harkins SS, Hariharan C, Wasserman H, Zandonatti MA, Miller R, Maule E, Kim K, Valentine KM, Shresta S, Saphire EO
Cell Rep (2023) 42 pp. 112421-112421 [ DOI: doi:10.1016/j.celrep.2023.112421 Pubmed: 37083327 ]
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Antibody 1c3 fab light chain (11 kDa, Protein from Homo sapiens)
- Antibody 1c3 fab heavy chain,antibody 1c3 fab light chain (Complex from Homo sapiens)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Antibody 1c3 fab heavy chain (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Structure of sars-cov-2 omicron ba.1 spike in complex with antibody 1c3 fab (Complex)
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8f0h
Q-score: 0.484
Hastie KM, Yu X, Ana-Sosa-Batiz F, Zyla DS, Harkins SS, Hariharan C, Wasserman H, Zandonatti MA, Miller R, Maule E, Kim K, Valentine KM, Shresta S, Saphire EO
Cell Rep (2023) 42 pp. 112421-112421 [ Pubmed: 37083327 DOI: doi:10.1016/j.celrep.2023.112421 ]
- Antibody fab 2a10 light chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Antibody fab 1h2 heavy chain (13 kDa, Protein from Homo sapiens)
- Antibody fab 1h2 heavy chain, antibody fab 1h2 light chain, antibody fab 2a10 heavy chain, antibody fab 2a10 light chain (Complex from Homo sapiens)
- Antibody fab 1h2 light chain (10 kDa, Protein from Homo sapiens)
- Structure of sars-cov-2 d614g spike in complex with antibody fabs 1h2 and 2a10 (Complex)
- Antibody fab 2a10 heavy chain (12 kDa, Protein from Homo sapiens)
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8dmh
Q-score: 0.515
Moon-Walker A, Zhang Z, Zyla DS, Buck TK, Li H, Diaz Avalos R, Schendel SL, Hastie KM, Crotty S, Saphire EO
Cell Chem Biol (2023) 30 pp. 403-411.e4 [ Pubmed: 36990092 DOI: doi:10.1016/j.chembiol.2023.03.005 ]
- Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody m28 (Complex)
- Glycoprotein g2,cobalamin adenosyltransferase-like domain-containing protein trimerization tag (42 kDa, Protein from Lymphocytic choriomeningitis virus)
- 18.5c-m28 fab light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glycoprotein (Complex from Lymphocytic choriomeningitis mammarenavirus)
- Glycoprotein g1 (25 kDa, Protein from Lymphocytic choriomeningitis virus)
- 18.5c-m28 fab heavy chain (23 kDa, Protein from Homo sapiens)
- 18.5c-m28 fab light chain, 18.5c-m28 fab heavy chain (Complex from Homo sapiens)
Lymphocytic choriomeningitis virus glycoprotein
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8dmi
Q-score: 0.454
Moon-Walker A, Zhang Z, Zyla DS, Buck TK, Li H, Diaz Avalos R, Schendel SL, Hastie KM, Crotty S, Saphire EO
Cell Chem Biol (2023) 30 pp. 403-411.e4 [ Pubmed: 36990092 DOI: doi:10.1016/j.chembiol.2023.03.005 ]
- Glycoprotein g1 (25 kDa, Protein from Lymphocytic choriomeningitis virus)
- Lymphocytic choriomeningitis virus glycoprotein (Complex from Lymphocytic choriomeningitis mammarenavirus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glycoprotein g2,cobalamin adenosyltransferase-like domain-containing protein trimerization tag (42 kDa, Protein from Lymphocytic choriomeningitis virus)