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Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8iht
Q-score: 0.345
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ DOI: doi:10.1038/s41422-023-00884-2 Pubmed: 37845487 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
XBB.1.5.70 spike protein in complex with ACE2
Resolution: 4.64 Å
EM Method: Single-particle
Fitted PDBs: 8wtj
Q-score: 0.202
Jian F, Feng L, Yang S, Yu Y, Wang L, Song W, Yisimayi A, Chen X, Xu Y, Wang P, Yu L, Wang J, Liu L, Niu X, Wang J, Xiao T, An R, Wang Y, Gu Q, Shao F, Jin R, Shen Z, Wang Y, Wang X, Cao Y
PLoS Pathog (2023) 19 pp. e1011868-e1011868 [ Pubmed: 38117863 DOI: doi:10.1371/journal.ppat.1011868 ]
- Spike glycoprotein (145 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (68 kDa, Protein from Homo sapiens)
- Xbb.1.5.70 spike protein in complex with hace2 (Complex)
- Spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Human ace2 (Complex from Homo sapiens)
XBB.1.5.10 spike protein in complex with ACE2
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8wro
Q-score: 0.193
Jian F, Feng L, Yang S, Yu Y, Wang L, Song W, Yisimayi A, Chen X, Xu Y, Wang P, Yu L, Wang J, Liu L, Niu X, Wang J, Xiao T, An R, Wang Y, Gu Q, Shao F, Jin R, Shen Z, Wang Y, Wang X, Cao Y
PLoS Pathog (2023) 19 pp. e1011868-e1011868 [ Pubmed: 38117863 DOI: doi:10.1371/journal.ppat.1011868 ]
- Processed angiotensin-converting enzyme 2 (68 kDa, Protein from Homo sapiens)
- Spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Human ace2 (Complex from Homo sapiens)
- Xbb.1.5.10 spike protein in complex with ace2 (Complex)
- Spike glycoprotein,spike glycoprotein,spike glycoprotein,fusion protein (145 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Sin3/rpd3/eaf3/rco1 (Complex)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (Complex from Saccharomyces cerevisiae S288C)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
Cryo-EM map of Rpd3S complex bound to H3K36me3 nucleosome in close state
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7yi4
Q-score: 0.23
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 rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Dna (Complex from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
- Histone h3 (Complex)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
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)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Dna (Complex from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
- Histone h3 (Complex)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of cryptophyte photosystem I
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 7y7b
Q-score: 0.607
Zhao LS, Wang P, Li K, Zhang QB, He FY, Li CY, Su HN, Chen XL, Liu LN, Zhang YZ
Plant Cell (2023) 35 pp. 2449-2463 [ Pubmed: 36943796 DOI: doi:10.1093/plcell/koad087 ]
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Acpi-3 (24 kDa, Protein from Chroomonas placoidea)
- Acpi-1 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Chroomonas placoidea)
- Psao (10 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Acpi-13/10 (22 kDa, Protein from Chroomonas placoidea)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Acpi-s (25 kDa, Protein from Chroomonas placoidea)
- Acpi-14 (23 kDa, Protein from Chroomonas placoidea)
- Psar (13 kDa, Protein from Chroomonas placoidea)
- Acpi-11 (22 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- Acpi-2 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chroomonas placoidea)
- Acpi-4 (23 kDa, Protein from Chroomonas placoidea)
- Iron/sulfur cluster (351 Da, Ligand)
- Acpi-5 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chroomonas placoidea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i of cryptophyte (890 kDa, Complex from Chroomonas placoidea)
- Acpi-6 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-8 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chroomonas placoidea)
- Acpi-12 (23 kDa, Protein from Chroomonas placoidea)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chroomonas placoidea)
- Unk1 (13 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Chroomonas placoidea)
- Acpi-7 (24 kDa, Protein from Chroomonas placoidea)
- Acpi-9 (27 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
Cryo-EM structure of cryptophyte photosystem I
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 7y8a
Q-score: 0.581
Zhao LS, Wang P, Li K, Zhang QB, He FY, Li CY, Su HN, Chen XL, Liu LN, Zhang YZ
Plant Cell (2023) 35 pp. 2449-2463 [ Pubmed: 36943796 DOI: doi:10.1093/plcell/koad087 ]
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Acpi-3 (24 kDa, Protein from Chroomonas placoidea)
- Acpi-1 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Acpi-s (25 kDa, Protein from Chroomonas placoidea)
- Acpi-14 (23 kDa, Protein from Chroomonas placoidea)
- Psar (13 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- Acpi-2 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chroomonas placoidea)
- Acpi-4 (23 kDa, Protein from Chroomonas placoidea)
- Iron/sulfur cluster (351 Da, Ligand)
- Acpi-13 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-5 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chroomonas placoidea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Acpi-6 (22 kDa, Protein from Chroomonas placoidea)
- Photosystem i of cryptophyte (Complex from Chroomonas placoidea)
- Acpi-8 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chroomonas placoidea)
- Acpi-12 (23 kDa, Protein from Chroomonas placoidea)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chroomonas placoidea)
- Unk1 (13 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Chroomonas placoidea)
- Acpi-7 (24 kDa, Protein from Chroomonas placoidea)
- Psao (16 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
Cryo-EM structure of Sr35 resistosome induced by AvrSr35 R381A
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7xx2
Q-score: 0.418
Zhao YB, Liu MX, Chen TT, Ma X, Li ZK, Zheng Z, Zheng SR, Chen L, Li YZ, Tang LR, Chen Q, Wang P, Ouyang S
Sci Adv (2022) 8 pp. eabq5108-eabq5108 [ Pubmed: 36083908 DOI: doi:10.1126/sciadv.abq5108 ]
- Avrsr35 (66 kDa, Protein from Puccinia graminis f. sp. tritici)
- Sr35 resistosome (Complex)
- Sr35 (Complex from Triticum monococcum)
- Cnl9 (105 kDa, Protein from Triticum monococcum)
- Avrsr35 (Complex from Puccinia graminis f.sp.tritici)
- Adenosine-5'-triphosphate (507 Da, Ligand)
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- [ Pubmed: 36270286 DOI: doi:10.1016/j.chom.2022.09.018 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba.2.75 s trimer in complex with s309 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba.2.75 s trimer (Complex from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S309 (Complex)
- S309 heavy chain (13 kDa, Protein from Homo sapiens)
- S309 light chain (23 kDa, Protein from Homo sapiens)