Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8fr6
Q-score: 0.528
Sastry M, Changela A, Gorman J, Xu K, Chuang GY, Shen CH, Cheng C, Geng H, O'Dell S, Ou L, Rawi R, Reveiz M, Stewart-Jones GBE, Wang S, Zhang B, Zhou T, Biju A, Chambers M, Chen X, Corrigan AR, Lin BC, Louder MK, McKee K, Nazzari AF, Olia AS, Parchment DK, Sarfo EK, Stephens T, Stuckey J, Tsybovsky Y, Verardi R, Wang Y, Zheng CY, Chen Y, Doria-Rose NA, McDermott AB, Mascola JR, Kwong PD
J Virol (2023) 97 pp. e0160422-e0160422 [ Pubmed: 37098956 DOI: doi:10.1128/jvi.01604-22 ]
- Envelope glycoprotein gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Antibody fab (Complex from Mus musculus)
- Vfp53.02 fab heavy chain (24 kDa, Protein from Mus musculus)
- Hiv-1 env trimer bg505 ds-sosip (Complex from Human immunodeficiency virus 1)
- Complex of antibody fab vfp53.02 with hiv-1 env trimer bg505 ds-sosip (Complex)
- Vfp53.02 fab light chain (24 kDa, Protein from Mus musculus)
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8gzz
Q-score: 0.491
Guo H, Yang Y, Zhao T, Lu Y, Gao Y, Li T, Xiao H, Chu X, Zheng L, Li W, Cheng H, Huang H, Liu Y, Lou Y, Nguyen HC, Wu C, Chen Y, Yang H, Ji X
Commun Biol (2023) 6 pp. 364-364 [ DOI: doi:10.1038/s42003-023-04759-5 Pubmed: 37012333 ]
- Rabbit monoclonal antibody 1h1 fab heavy chain (12 kDa, Protein from Oryctolagus cuniculus)
- Omicron spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rabbit monoclonal antibody 1h1 fab light chain (11 kDa, Protein from Oryctolagus cuniculus)
- Sars-cov-2 omicron spike glycoprotein complex with 55a8 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 1h1 fab (Complex)
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8h00
Q-score: 0.484
Guo H, Yang Y, Zhao T, Lu Y, Gao Y, Li T, Xiao H, Chu X, Zheng L, Li W, Cheng H, Huang H, Liu Y, Lou Y, Nguyen HC, Wu C, Chen Y, Yang H, Ji X
Commun Biol (2023) 6 pp. 364-364 [ DOI: doi:10.1038/s42003-023-04759-5 Pubmed: 37012333 ]
- Rabbit monoclonal antibody 1h1 fab heavy chain (12 kDa, Protein from Oryctolagus cuniculus)
- Omicron spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rabbit monoclonal antibody 1h1 fab light chain (11 kDa, Protein from Oryctolagus cuniculus)
- Sars-cov-2 omicron spike glycoprotein complex with 55a8 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 1h1 fab (Complex)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8h01
Q-score: 0.342
Guo H, Yang Y, Zhao T, Lu Y, Gao Y, Li T, Xiao H, Chu X, Zheng L, Li W, Cheng H, Huang H, Liu Y, Lou Y, Nguyen HC, Wu C, Chen Y, Yang H, Ji X
Commun Biol (2023) 6 pp. 364-364 [ DOI: doi:10.1038/s42003-023-04759-5 Pubmed: 37012333 ]
- Rabbit monoclonal antibody 1h1 fab heavy chain (12 kDa, Protein from Oryctolagus cuniculus)
- Omicron spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rabbit monoclonal antibody 1h1 fab light chain (11 kDa, Protein from Oryctolagus cuniculus)
- Sars-cov-2 omicron spike glycoprotein complex with 55a8 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 1h1 fab (Complex)
S728-1157 IgG in complex with SARS-CoV-2-6P-Mut7 Spike protein (focused refinement)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8d0z
Q-score: 0.42
Changrob S, Halfmann PJ, Liu H, Torres JL, McGrath JJC, Ozorowski G, Li L, Wilbanks GD, Kuroda M, Maemura T, Huang M, Zheng NY, Turner HL, Erickson SA, Fu Y, Yasuhara A, Singh G, Monahan B, Mauldin J, Srivastava K, Simon V, Krammer F, Sather DN, Ward AB, Wilson IA, Kawaoka Y, Wilson PC
J Clin Inv (2023) 133 [ Pubmed: 36862518 DOI: doi:10.1172/JCI166844 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S728-1157 fab heavy chain variable region (12 kDa, Protein from Homo sapiens)
- S728-1157 fab light chain variable region (11 kDa, Protein from Homo sapiens)
- S728-1157 igg in complex with sars-cov-2-6p-mut7 s protein (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ek1
Q-score: 0.473
Tripathi P, Bender MF, Lei H, Da Silva Pereira L, Shen CH, Bonilla B, Dillon M, Ou L, Pancera M, Wang LT, Zhang B, Batista FD, Idris AH, Seder RA, Kwong PD
Structure (2023) 31 pp. 480-491.e4 [ Pubmed: 36931276 DOI: doi:10.1016/j.str.2023.02.009 ]
- Pfcsp in complex with antibody l9 (Complex from Homo sapiens)
- Circumsporozoite protein (37 kDa, Protein from Plasmodium falciparum 3D7)
- L9 fab light chain (23 kDa, Protein from Homo sapiens)
- L9 fab heavy chain (24 kDa, Protein from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8eka
Q-score: 0.486
Tripathi P, Bender MF, Lei H, Da Silva Pereira L, Shen CH, Bonilla B, Dillon M, Ou L, Pancera M, Wang LT, Zhang B, Batista FD, Idris AH, Seder RA, Kwong PD
Structure (2023) 31 pp. 480-491.e4 [ Pubmed: 36931276 DOI: doi:10.1016/j.str.2023.02.009 ]
- Pfcsp in complex with antibody l9 (Complex from Homo sapiens)
- Circumsporozoite protein (37 kDa, Protein from Plasmodium falciparum 3D7)
- L9 fab light chain (23 kDa, Protein from Homo sapiens)
- L9 fab heavy chain (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Delta Spike in complex with FP-12A
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8hhx
Q-score: 0.301
Huang KA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C
Nat Commun (2023) 14 pp. 311-311 [ DOI: doi:10.1038/s41467-023-35949-8 Pubmed: 36658148 ]
- Complex of delta spike and fp-12a with two fabs bound to one spike in 3-rbd-up conformation (550 kDa, Complex)
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 delta spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fp-12a (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fp-12a fab heavy chain (23 kDa, Protein from Homo sapiens)
- Fp-12a fab light chain (23 kDa, Protein from Homo sapiens)
SARS-CoV-2 Delta Spike in complex with IS-9A
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8hhy
Q-score: 0.313
Huang KA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C
Nat Commun (2023) 14 pp. 311-311 [ DOI: doi:10.1038/s41467-023-35949-8 Pubmed: 36658148 ]
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Is-9a fab (Complex from Homo sapiens)
- Is-9a fab heavy chain (24 kDa, Protein from Homo sapiens)
- Complex of delta spike and is-9a with two fabs bound to one spike in 3-rbd-up conformation (550 kDa, Complex)
- Is-9a fab light chain (23 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
Resolution: 4.28 Å
EM Method: Single-particle
Fitted PDBs: 8hhz
Q-score: 0.207
Huang KA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C
Nat Commun (2023) 14 pp. 311-311 [ DOI: doi:10.1038/s41467-023-35949-8 Pubmed: 36658148 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 delta spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Complex of delta spike and iy-2a with two fabs bound to one spike in 3-rbd-up conformation (550 kDa, Complex)
- Iy-2a fab heavy chain (23 kDa, Protein from Homo sapiens)
- Iy-2a fab light chain (23 kDa, Protein from Homo sapiens)
- Iy-2a (Complex from Homo sapiens)