Cryo-EM map of Rpd3S in loose-state Rpd3S-NCP complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7yi2
Q-score: 0.483
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ DOI: doi:10.1038/s41586-023-06349-1 Pubmed: 37468628 ]
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Sin3/rpd3/eaf3/rco1 (Complex)
- Dna (Complex from Saccharomyces cerevisiae S288C)
Cryo-EM msp of Rpd3S complex bound to H3K36me3 nucleosome in loose state
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7yi5
Q-score: 0.254
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ DOI: doi:10.1038/s41586-023-06349-1 Pubmed: 37468628 ]
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Dna (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h3 (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state1)
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 7yqx
Q-score: 0.353
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ DOI: doi:10.1016/j.chom.2022.09.018 Pubmed: 36270286 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S309 (Complex)
- S309 heavy chain (13 kDa, Protein from Homo sapiens)
- S309 light chain (23 kDa, Protein from Homo sapiens)
- Ba.2.75 s trimer (Complex from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba.2.75 s trimer in complex with s309 (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state2)
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 7yqy
Q-score: 0.352
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ DOI: doi:10.1016/j.chom.2022.09.018 Pubmed: 36270286 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba.2.75 s trimer in complex with s309 (Complex from Homo sapiens)
- S309 light chain (23 kDa, Protein from Homo sapiens)
- S309 heavy chain (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state3)
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 7yqz
Q-score: 0.382
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ Pubmed: 36270286 DOI: doi:10.1016/j.chom.2022.09.018 ]
- S309 light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S309 (Complex)
- S309 heavy chain (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ba.2.75 s trimer (Complex from Homo sapiens)
- Ba.2.75 s trimer in complex with s309 (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 BA.2.75 S Trimer in complex with XG2v024
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 7yr1
Q-score: 0.459
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ DOI: doi:10.1016/j.chom.2022.09.018 Pubmed: 36270286 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba.2.75 s trimer in complex with xg2v024 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Xg2v024 light chain (11 kDa, Protein from Homo sapiens)
- Xg2v024 heavy/light chains (Complex)
- Xg2v024 heavy chain (13 kDa, Protein from Homo sapiens)
- Ba.2.75 s trimer (Complex from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of NTD-directed neutralizing antibody 4-8 Fab in complex with SARS-CoV-2 S2P spike
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 7lqv
Q-score: 0.318
Cerutti G, Guo Y, ZHou T, Gorman J, Lee M, Rapp M, Reddem ER, Yu J, Bahna F, Bimela J, Huang Y, Katsamba PS, Liu L, Nair MS, Rawi R, Olia AS, Wang P, Zhang B, Chuang GY, Ho DD, Sheng Z, Kwong PD, Shapiro L
Cell Host Microbe (2021) [ DOI: doi:10.1016/j.chom.2021.03.005 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 4-8 fab in complex with sars-cov-2 s2p spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- 4-8 heavy chain (13 kDa, Protein from Homo sapiens)
- 4-8 light chain (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 7kne
Q-score: 0.253
Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schon A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD
Cell Host Microbe (2020) 28 pp. 867-879.e5 [ DOI: doi:10.1016/j.chom.2020.11.004 Pubmed: 33271067 ]
- Single ace2-bound sars-cov-2 trimer spike at ph 5.5 (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 7kmz
Q-score: 0.285
Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schon A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD
Cell Host Microbe (2020) 28 pp. 867-879.e5 [ DOI: doi:10.1016/j.chom.2020.11.004 Pubmed: 33271067 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Cryo-em structure of double ace2-bound sars-cov-2 trimer spike at ph 7.4 (Complex from Severe acute respiratory syndrome coronavirus 2)