Electron Microscopy Data Bank

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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 [ DOI: doi:10.1038/s41594-023-01023-6 Pubmed: 37430064 ]

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 [ DOI: doi:10.1038/s41594-023-01023-6 Pubmed: 37430064 ]

Sample:

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

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 [ DOI: doi:10.1038/s41594-023-01023-6 Pubmed: 37430064 ]

Sample:

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)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

EMD-29016

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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-33189

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cryo-EM structure of hemoglobin

Release date: Nov. 9, 2022
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7xgy
Q-score: 0.407

Zheng L, Liu N, Gao X, Zhu W, Liu K, Wu C, Yan R, Zhang J, Gao X, Yao Y, Deng B, Xu J, Lu Y, Liu Z, Li M, Wei X, Wang HW, Peng H

Nat Methods (2023) 20 pp. 123-130 [ DOI: doi:10.1038/s41592-022-01693-y Pubmed: 36522503 ]

Sample:

Protoporphyrin ix containing fe (616 Da, Ligand)
Hemoglobin (Complex from Homo sapiens)
Hemoglobin subunit beta (16 kDa, Protein from Homo sapiens)
Hemoglobin subunit alpha (15 kDa, Protein from Homo sapiens)

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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)

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