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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Calcium ion (40 Da, Ligand)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
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 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)
- 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)
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)
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 ]
- Acpi-8 (23 kDa, Protein from Chroomonas placoidea)
- Psao (10 kDa, Protein from Chroomonas placoidea)
- Unk1 (13 kDa, Protein from Chroomonas placoidea)
- Acpi-13/10 (22 kDa, Protein from Chroomonas placoidea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Chroomonas placoidea)
- Acpi-12 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-1 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i of cryptophyte (890 kDa, Complex from Chroomonas placoidea)
- Psar (13 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chroomonas placoidea)
- Acpi-7 (24 kDa, Protein from Chroomonas placoidea)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chroomonas placoidea)
- Acpi-s (25 kDa, Protein from Chroomonas placoidea)
- Acpi-3 (24 kDa, Protein from Chroomonas placoidea)
- Acpi-6 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-14 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-11 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-4 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-2 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xi (16 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~{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)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- (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)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Acpi-9 (27 kDa, Protein from Chroomonas placoidea)
- Acpi-5 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 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)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chroomonas placoidea)
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 ]
- Acpi-8 (23 kDa, Protein from Chroomonas placoidea)
- Unk1 (13 kDa, Protein from Chroomonas placoidea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Chroomonas placoidea)
- Acpi-12 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-1 (23 kDa, Protein from Chroomonas placoidea)
- Psar (13 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chroomonas placoidea)
- Acpi-7 (24 kDa, Protein from Chroomonas placoidea)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chroomonas placoidea)
- Acpi-s (25 kDa, Protein from Chroomonas placoidea)
- Acpi-3 (24 kDa, Protein from Chroomonas placoidea)
- Acpi-6 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-14 (23 kDa, Protein from Chroomonas placoidea)
- Psao (16 kDa, Protein from Chroomonas placoidea)
- Acpi-13 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-4 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i of cryptophyte (Complex from Chroomonas placoidea)
- Acpi-2 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xi (16 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~{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)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- (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)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Acpi-5 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 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)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chroomonas placoidea)
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 [ DOI: doi:10.1126/sciadv.abq5108 Pubmed: 36083908 ]
- Sr35 resistosome (Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Avrsr35 (66 kDa, Protein from Puccinia graminis f. sp. tritici)
- Avrsr35 (Complex from Puccinia graminis f.sp.tritici)
- Cnl9 (105 kDa, Protein from Triticum monococcum)
- Sr35 (Complex from Triticum monococcum)
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- [ 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)