Electron Microscopy Data Bank

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SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7

Release date: Aug. 2, 2023
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 7y71
Q-score: 0.415

Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF

Sci Adv (2023) 9 pp. eade3470-eade3470 [ DOI: doi:10.1126/sciadv.ade3470 Pubmed: 37494438 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Sars-cov-2 spike glycoprotein trimer complexed with fab fragment of anti-rbd antibody e7 (Complex from Homo sapiens)
Fab e7 heavy chain (23 kDa, Protein from Homo sapiens)
Spike glycoprotein (132 kDa, Protein from Homo sapiens)
Fab e7 light chain (23 kDa, Protein from Homo sapiens)

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EMD-33651

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SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface)

Release date: Aug. 2, 2023
Resolution: 4.03 Å
EM Method: Single-particle
Fitted PDBs: 7y72
Q-score: 0.395

Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF

Sci Adv (2023) 9 pp. eade3470-eade3470 [ DOI: doi:10.1126/sciadv.ade3470 Pubmed: 37494438 ]

Sample:

Fab e7 heavy chain (23 kDa, Protein from Homo sapiens)
Sars-cov-2 spike glycoprotein trimer complexed with fab fragment of anti-rbd antibody e7 (Complex from Homo sapiens)
Spike glycoprotein (132 kDa, Protein from Homo sapiens)
Fab e7 light chain (23 kDa, Protein from Homo sapiens)

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EMD-27205

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Closed state of SARS-CoV-2 BA.2 variant spike protein

Release date: June 7, 2023
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8d55
Q-score: 0.434

Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B

Nat Struct Mol Biol (2023) 30 pp. 980-990 [ Pubmed: 37430064 DOI: doi:10.1038/s41594-023-01023-6 ]

Sample:

Closed state of pre-fusion sars-cov-2 ba.2 variant spike protein (600 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-27206

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One RBD-up state of SARS-CoV-2 BA.2 variant spike protein

Release date: June 7, 2023
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8d56
Q-score: 0.438

Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B

Nat Struct Mol Biol (2023) 30 pp. 980-990 [ Pubmed: 37430064 DOI: doi:10.1038/s41594-023-01023-6 ]

Sample:

One rbd-up state of pre-fusion sars-cov-2 ba.2 variant spike protein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-27207

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Middle state of SARS-CoV-2 BA.2 variant spike protein

Release date: June 7, 2023
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d5a
Q-score: 0.414

Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B

Nat Struct Mol Biol (2023) 30 pp. 980-990 [ Pubmed: 37430064 DOI: doi:10.1038/s41594-023-01023-6 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Middle state of pre-fusion sars-cov-2 ba.2 variant spike protein (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-26021

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Structural and functional impact by SARS-CoV-2 Omicron spike mutations

Release date: Feb. 16, 2022
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7tnw
Q-score: 0.44

Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B

Cell Rep (2022) 39 pp. 110729-110729 [ Pubmed: 35452593 DOI: doi:10.1016/j.celrep.2022.110729 ]

Sample:

Closed state of pre-fusion sars-cov-2 omicron variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-26029

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Structural and functional impact by SARS-CoV-2 Omicron spike mutations

Release date: Feb. 16, 2022
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7to4
Q-score: 0.394

Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B

Cell Rep (2022) 39 pp. 110729-110729 [ Pubmed: 35452593 DOI: doi:10.1016/j.celrep.2022.110729 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
One rbd-up state of pre-fusion sars-cov-2 omicron variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-24982

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One RBD-up 1 of pre-fusion SARS-CoV-2 Delta variant spike protein

Release date: Nov. 10, 2021
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7sbl
Q-score: 0.394

Zhang J, Xiao T, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Walsh Jr RM, Rits-Volloch S, Wesemann DR, Yang W, Seaman MS, Lu J, Chen B

Science (2021) 374 pp. 1353-1360 [ Pubmed: 34698504 DOI: doi:10.1126/science.abl9463 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
One rbd-up 1 of pre-fusion sars-cov-2 delta variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-24988

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One RBD-up 2 of pre-fusion SARS-CoV-2 Gamma variant spike protein

Release date: Nov. 10, 2021
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7sbt
Q-score: 0.269

Zhang J, Xiao T, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Walsh Jr RM, Rits-Volloch S, Wesemann DR, Yang W, Seaman MS, Lu J, Chen B

Science (2021) 374 pp. 1353-1360 [ Pubmed: 34698504 DOI: doi:10.1126/science.abl9463 ]

Sample:

One rbd-up 2 of pre-fusion sars-cov-2 gamma variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

EMD-24981

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Closed state of pre-fusion SARS-CoV-2 Delta variant spike protein

Release date: Nov. 3, 2021
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7sbk
Q-score: 0.434

Zhang J, Xiao T, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Walsh Jr RM, Rits-Volloch S, Wesemann DR, Yang W, Seaman MS, Lu J, Chen B

Science (2021) 374 pp. 1353-1360 [ Pubmed: 34698504 DOI: doi:10.1126/science.abl9463 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Closed state of pre-fusion sars-cov-2 delta variant spike protein (440 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)

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