Electron Microscopy Data Bank

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SARS-CoV-2 C.1.2 variant spike (Open state)

Release date: Nov. 29, 2023
Resolution: 3.82 Å
EM Method: Single-particle
Fitted PDBs: 7ybn
Q-score: 0.376

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 lambda variant spike (Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-33724

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SARS-CoV-2 B.1.620 variant spike (open state)

Release date: Sept. 6, 2023
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7ybk
Q-score: 0.319

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Sars-cov-2 b.1.620 variant spike (open state) (Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-33721

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SARS-CoV-2 lambda variant spike

Release date: Aug. 9, 2023
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7ybh
Q-score: 0.347

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 lambda variant spike (Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

EMD-33725

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SARS-CoV-2 B.1.620 variant spike (close state)

Release date: Aug. 9, 2023
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ybl
Q-score: 0.178

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Sars-cov-2 b.1.620 variant spike (close state) (Complex from Severe acute respiratory syndrome coronavirus 2)

EMD-33726

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SARS-CoV-2 C.1.2 variant spike (Close state)

Release date: Aug. 9, 2023
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7ybm
Q-score: 0.303

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 c.1.2 variant spike (close state) (Complex from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

EMD-33722

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SARS-CoV-2 Mu variant spike (open state)

Release date: July 12, 2023
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7ybi
Q-score: 0.331

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

Sars-cov-2 mu variant spike (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-33723

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SARS-CoV-2 Mu variant spike(close state)

Release date: July 12, 2023
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 7ybj
Q-score: 0.35

Xing X, Wang L, Cui Z, Fu W, Zheng T, Qin L, Ge P, Qian A, Wang N, Yuan S

Virol Sin (2022) 37 pp. 938-941 [ Pubmed: 36368512 DOI: doi:10.1016/j.virs.2022.11.003 ]

Sample:

EMD-32873

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ICP1 Csy complex

Release date: April 26, 2023
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7wwu
Q-score: 0.413

Zhang M, Peng R, Peng Q, Liu S, Li Z, Zhang Y, Song H, Yang J, Xing X, Wang P, Qi J, Gao GF

PNAS (2023) 120 pp. e2215098120-e2215098120 [ Pubmed: 37094126 DOI: doi:10.1073/pnas.2215098120 ]

Sample:

Csy4 (21 kDa, Protein from Vibrio phage ICP1 2011 A)
Csy2 (29 kDa, Protein from Vibrio phage ICP1 2011 A)
Csy3 (35 kDa, Protein from Vibrio phage ICP1 2011 A)
Guide-rna (19 kDa, RNA from Vibrio phage ICP1 2011 A)
Apo-icp1 csy complex (Complex from Vibrio phage ICP1 2011 A)
Csy1 (22 kDa, Protein from Vibrio phage ICP1 2011 A)

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EMD-32874

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DNA bound-ICP1 Csy complex

Release date: April 26, 2023
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7wwv
Q-score: 0.484

Zhang M, Peng R, Peng Q, Liu S, Li Z, Zhang Y, Song H, Yang J, Xing X, Wang P, Qi J, Gao GF

PNAS (2023) 120 pp. e2215098120-e2215098120 [ Pubmed: 37094126 DOI: doi:10.1073/pnas.2215098120 ]

Sample:

Guide-rna (19 kDa, RNA from Vibrio phage ICP1 2011 A)
Non-target strand dna (18 kDa, DNA from Vibrio phage ICP1 2011 A)
Csy2 (29 kDa, Protein from Vibrio phage ICP1 2011 A)
Target dna bound icp1 csy complex (Complex from Vibrio phage ICP1 2011 A)
Csy3 (35 kDa, Protein from Vibrio phage ICP1 2011 A)
Csy1 (22 kDa, Protein from Vibrio phage ICP1 2011 A)
Target strand dna (18 kDa, DNA from Vibrio phage ICP1 2011 A)

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