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-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-32678

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Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies

Release date: March 8, 2023
Resolution: 3.88 Å
EM Method: Single-particle
Fitted PDBs: 7wp8
Q-score: 0.441

Wu Y, Wang S, Zhang Y, Yuan L, Zheng Q, Wei M, Shi Y, Wang Z, Ma J, Wang K, Nie M, Xiao J, Huang Z, Chen P, Guo H, Lan M, Xu J, Hou W, Hong Y, Chen D, Sun H, Xiong H, Zhou M, Liu C, Guo W, Guo H, Gao J, Gan C, Li Z, Zhang H, Wang X, Li S, Cheng T, Zhao Q, Chen Y, Wu T, Zhang T, Zhang J, Cao H, Zhu H, Yuan Q, Guan Y, Xia N

Cell Host Microbe (2022) 30 pp. 1732-1744.e7 [ Pubmed: 36323313 DOI: doi:10.1016/j.chom.2022.10.011 ]

Sample:

83h7 heavy chain (13 kDa, Protein from Mus musculus)
Cryo-em structure of sars-cov-2 recombinant spike protein stfk1628x in complex with three neutralizing antibodies (Complex from Mus musculus)
Neutralizing antibodies (Complex from Severe acute respiratory syndrome coronavirus 2)
2b4 light chain (12 kDa, Protein from Mus musculus)
Spike protein stfk1628x (Complex)
85f7 heavy chain (13 kDa, Protein from Mus musculus)
85f7 light chain (11 kDa, Protein from Mus musculus)
83h7 light chain (11 kDa, Protein from Mus musculus)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (20 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2b4 heavy chain (13 kDa, Protein from Mus musculus)

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EMD-32676

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Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies

Release date: March 1, 2023
Resolution: 3.81 Å
EM Method: Single-particle
Fitted PDBs: 7wp6
Q-score: 0.438

Wu Y, Wang S, Zhang Y, Yuan L, Zheng Q, Wei M, Shi Y, Wang Z, Ma J, Wang K, Nie M, Xiao J, Huang Z, Chen P, Guo H, Lan M, Xu J, Hou W, Hong Y, Chen D, Sun H, Xiong H, Zhou M, Liu C, Guo W, Guo H, Gao J, Gan C, Li Z, Zhang H, Wang X, Li S, Cheng T, Zhao Q, Chen Y, Wu T, Zhang T, Zhang J, Cao H, Zhu H, Yuan Q, Guan Y, Xia N

Cell Host Microbe (2022) 30 pp. 1732-1744.e7 [ Pubmed: 36323313 DOI: doi:10.1016/j.chom.2022.10.011 ]

Sample:

83h7 heavy chain (13 kDa, Protein from Mus musculus)
36h6 light chain (12 kDa, Protein from Mus musculus)
Spike protein stfk (Complex)
Neutralizing antibodies (Complex from Severe acute respiratory syndrome coronavirus 2)
Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
85f7 heavy chain (13 kDa, Protein from Mus musculus)
85f7 light chain (11 kDa, Protein from Mus musculus)
36h6 heavy chain (13 kDa, Protein from Mus musculus)
83h7 light chain (11 kDa, Protein from Mus musculus)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-em structure of sars-cov-2 recombinant spike protein stfk in complex with three neutralizing antibodies (Complex from Mus musculus)

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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)

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