Electron Microscopy Data Bank

EMD-40190

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Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer

Release date: March 27, 2024
Resolution: 3.9 Å
EM Method: Single-particle

Liu WP, Shokr A, Mabrouk M, Aly N, Zhang J, Aschauer P, Gao HL, Selvaraj G, Elzoghby A, Chen B, Kawano T, Nasr ML

To Be Published

Sample:

Local map of b3sb3l in complex with two-rbd-up state i of soluble sars-cov-2 spike trimer (600 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)

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-0734

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Spinach 80S ribosome

Release date: Aug. 12, 2020
Resolution: 34.0 Å
EM Method: Subtomogram averaging

Zhang J, Zhang D, Sun L, Ji G, Huang X, Niu T, Xu J, Ma C, Zhu Y, Gao N, Xu W, Sun F

J Struct Biol (2021) 213 pp. 107763-107763 [ Pubmed: 34174447 DOI: doi:10.1016/j.jsb.2021.107763 ]

Sample:

Spinach 80s ribosome (Complex from Spinacia olerac)

EMD-6483

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Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps

Release date: Feb. 24, 2016
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 3jbu
Q-score: 0.341

Zhang J, Pan XJ, Yan KG, Sun S, Gao N, Sui SF

eLife (2015) 4 [ Pubmed: 26670735 DOI: doi:10.7554/eLife.09684 ]

Sample:

Secm-gly-rnc(ribosome-nascent-peptide-complex) complex with 50s mask (2 MDa, Sample)
Secm-gly-rnc with 50s mask (2 MDa, Complex from Escherichia coli)

EMD-6484

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Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps

Release date: Feb. 24, 2016
Resolution: 3.73 Å
EM Method: Single-particle

Zhang J, Pan XJ, Yan KG, Sun S, Gao N, Sui SF

eLife (2015) 4 [ Pubmed: 26670735 DOI: doi:10.7554/eLife.09684 ]

Sample:

Secm-gly-rnc(ribosome-nascent-peptide-complex) complex without mask (2 MDa, Sample)
Secm-gly-rnc without mask (2 MDa, Complex from Escherichia coli)

EMD-6485

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Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps

Release date: Feb. 24, 2016
Resolution: 3.32 Å
EM Method: Single-particle

Zhang J, Pan XJ, Yan KG, Sun S, Gao N, Sui SF

eLife (2015) 4 [ Pubmed: 26670735 DOI: doi:10.7554/eLife.09684 ]

Sample:

Secm-pro-rnc(ribosome-nascent-peptide-complex) complex without mask (2 MDa, Sample)
Secm-pro-rnc without mask (2 MDa, Complex from Escherichia coli)

EMD-6486

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Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps

Release date: Feb. 24, 2016
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 3jbv
Q-score: 0.394

Zhang J, Pan XJ, Yan KG, Sun S, Gao N, Sui SF

eLife (2015) 4 [ Pubmed: 26670735 DOI: doi:10.7554/eLife.09684 ]

Sample:

Secm-pro-rnc(ribosome-nascent-peptide-complex) complex with 50s mask (2 MDa, Sample)
Secm-pro-rnc with 50s mask (2 MDa, Complex from Escherichia coli)

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