Electron Microscopy Data Bank

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Structure of the asymmetric unit of SFTSV virion

Release date: Sept. 13, 2023
Resolution: 5.2 Å
EM Method: Single-particle
Fitted PDBs: 8i4t
Q-score: 0.206

Du S, Peng R, Xu W, Qu X, Wang Y, Wang J, Li L, Tian M, Guan Y, Wang J, Wang G, Li H, Deng L, Shi X, Ma Y, Liu F, Sun M, Wei Z, Jin N, Liu W, Qi J, Liu Q, Liao M, Li C

Nat Commun (2023) 14 pp. 6333-6333 [ DOI: doi:10.1038/s41467-023-41804-7 Pubmed: 37816705 ]

Sample:

Dabie bandavirus (Virus from Dabie bandavirus)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Envelopment polyprotein (54 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
Envelopment polyprotein (61 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)

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EMD-35540

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Structure of SFTSV Gn-Gc heterodimer

Release date: Sept. 13, 2023
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8ilq
Q-score: 0.419

Du S, Peng R, Xu W, Qu X, Wang Y, Wang J, Li L, Tian M, Guan Y, Wang J, Wang G, Li H, Deng L, Shi X, Ma Y, Liu F, Sun M, Wei Z, Jin N, Liu W, Qi J, Liu Q, Liao M, Li C

Nat Commun (2023) 14 pp. 6333-6333 [ DOI: doi:10.1038/s41467-023-41804-7 Pubmed: 37816705 ]

Sample:

2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Envelopment polyprotein (61 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
Envelopment polyprotein (54 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
Dabie bandavirus (Virus from Dabie bandavirus)

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EMD-33241

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Cryo-EM Structure of Human Niacin Receptor HCA2-Gi protein complex

Release date: Feb. 22, 2023
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk2
Q-score: 0.471

Yang Y, Kang HJ, Gao R, Wang J, Han GW, DiBerto JF, Wu L, Tong J, Qu L, Wu Y, Pileski R, Li X, Zhang XC, Zhao S, Kenakin T, Wang Q, Stevens RC, Peng W, Roth BL, Rao Z, Liu ZJ

Nat Commun (2023) 14 pp. 1692-1692 [ Pubmed: 36973264 DOI: doi:10.1038/s41467-023-37177-6 ]

Sample:

Hydroxycarboxylic acid receptor 2 (38 kDa, Protein from Homo sapiens)
2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid (386 Da, Ligand)
Scfv16 (26 kDa, Protein from Homo sapiens)
Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
Niacin receptor hca2-gi complex (Complex from Homo sapiens)
Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)

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EMD-33453

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Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-1 Conformation

Release date: July 20, 2022
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7xtz
Q-score: 0.588

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Linoleic acid (280 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)

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EMD-33454

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Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-211 Conformation

Release date: July 20, 2022
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7xu0
Q-score: 0.569

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Linoleic acid (280 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)

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EMD-33455

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Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-122 Conformation

Release date: July 20, 2022
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7xu1
Q-score: 0.548

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Linoleic acid (280 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)

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EMD-33456

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Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation

Release date: July 20, 2022
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xu2
Q-score: 0.523

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Linoleic acid (280 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)

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EMD-33457

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Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation

Release date: July 20, 2022
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7xu3
Q-score: 0.484

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-33458

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Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation

Release date: July 20, 2022
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xu4
Q-score: 0.511

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Linoleic acid (280 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)

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EMD-33459

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Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation

Release date: July 20, 2022
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xu5
Q-score: 0.509

Qu K, Chen Q, Ciazynska KA, Liu B, Zhang X, Wang J, He Y, Guan J, He J, Liu T, Zhang X, Carter AP, Xiong X, Briggs JAG

PLoS Pathog (2022) 18 pp. e1010583-e1010583 [ Pubmed: 35905112 DOI: doi:10.1371/journal.ppat.1010583 ]

Sample:

Biliverdine ix alpha (582 Da, Ligand)
Severe acute respiratory syndrome coronavirus 2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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