Electron Microscopy Data Bank

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Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane

Release date: May 10, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8fdw
Q-score: 0.327

Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B

Nature (2023) 619 pp. 403-409 [ Pubmed: 37285872 DOI: doi:10.1038/s41586-023-06273-4 ]

Sample:

Spike protein s2 (68 kDa, Protein from Severe acute respiratory syndrome coronavirus)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Sras-cov-2 postfusion spike protein in nanodisc (210 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Alpha-d-mannopyranose (180 Da, Ligand)

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EMD-29017

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Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane

Release date: May 10, 2023
Resolution: 3.4 Å
EM Method: Single-particle

Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B

Nature (2023) 619 pp. 403-409 [ Pubmed: 37285872 DOI: doi:10.1038/s41586-023-06273-4 ]

Sample:

Local map of sras-cov-2 postfusion spike protein in nanodisc from data set i (210 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-29018

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Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane

Release date: May 10, 2023
Resolution: 3.3 Å
EM Method: Single-particle

Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B

Nature (2023) 619 pp. 403-409 [ Pubmed: 37285872 DOI: doi:10.1038/s41586-023-06273-4 ]

Sample:

Local map of sras-cov-2 postfusion spike protein in nanodisc from combined data (210 kDa, Complex 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 [ DOI: doi:10.1016/j.celrep.2022.110729 Pubmed: 35452593 ]

Sample:

Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Closed state of pre-fusion sars-cov-2 omicron variant spike protein (440 MDa, Complex 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 [ DOI: doi:10.1016/j.celrep.2022.110729 Pubmed: 35452593 ]

Sample:

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

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 [ DOI: doi:10.1126/science.abl9463 Pubmed: 34698504 ]

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 [ DOI: doi:10.1126/science.abl9463 Pubmed: 34698504 ]

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)
Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

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 [ DOI: doi:10.1126/science.abl9463 Pubmed: 34698504 ]

Sample:

Closed state of pre-fusion sars-cov-2 delta 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-24983

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

Release date: Nov. 3, 2021
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7sbo
Q-score: 0.266

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 [ DOI: doi:10.1126/science.abl9463 Pubmed: 34698504 ]

Sample:

One rbd-up 2 of pre-fusion sars-cov-2 delta 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-24984

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

Release date: Nov. 3, 2021
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7sbp
Q-score: 0.427

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 [ DOI: doi:10.1126/science.abl9463 Pubmed: 34698504 ]

Sample:

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

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