Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8k9q
Q-score: 0.563
Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D
Nat Commun (2024) 15 pp. 8-8 [ DOI: doi:10.1038/s41467-023-44568-2 Pubmed: 38167496 ]
- Gpi inositol-deacylase,fused thermostable green fluorescent protein (163 kDa, Protein from synthetic construct)
- Gpi inositol-deacylase (163 kDa, Complex from Thermochaetoides thermophila)
- (2~{s})-2-azanyl-3-[[(2~{r})-3-hexadecanoyloxy-2-[(~{z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid (762 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 8k9r
Q-score: 0.604
Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D
Nat Commun (2024) 15 pp. 8-8 [ DOI: doi:10.1038/s41467-023-44568-2 Pubmed: 38167496 ]
- Alpha-d-mannopyranose (180 Da, Ligand)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- 2-azanylethyl [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate (303 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- Cholesterol (386 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Complex of the gpi inositol-deacylase with a chimera gpi-anchored protein (194 kDa, Complex from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- [(2~{r})-1-octadecoxy-3-[oxidanyl-[(2~{r},3~{r},5~{s},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate (853 Da, Ligand)
Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8k9t
Q-score: 0.585
Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D
Nat Commun (2024) 15 pp. 8-8 [ DOI: doi:10.1038/s41467-023-44568-2 Pubmed: 38167496 ]
- Alpha-d-mannopyranose (180 Da, Ligand)
- [(2~{r})-1-octadecoxy-3-[oxidanyl-[(2~{r},3~{r},5~{s},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{z},8~{z},11~{z},14~{z})-icosa-5,8,11,14-tetraenoate (873 Da, Ligand)
- 2-azanylethyl [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate (303 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- Complex of pgap1 with a chimera gpi-anchored protein (194 kDa, Complex from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- Palmitic acid (256 Da, Ligand)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8tdv
Q-score: 0.368
Orris B, Sung MW, Bhat S, Xu Y, Huynh KW, Han S, Johnson DC, Bosbach B, Shields DJ, Stivers JT
Nucleic Acids Res (2023) 51 pp. 12443-12458 [ Pubmed: 37930833 DOI: doi:10.1093/nar/gkad971 ]
- Rna (Complex)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (72 kDa, Protein from Homo sapiens)
- Deoxynucleoside triphosphate triphosphohydrolase samhd1 (Complex from Homo sapiens)
- Rna (5'-r(p*cp*cp*gp*ap*cp*cp*c)-3') (2 kDa, RNA from Virus-associated RNAs)
- Ssrna bound samhd1 t closed (Complex)
- Rna (5'-r(p*cp*cp*gp*gp*cp*c)-3') (1 kDa, RNA from Virus-associated RNAs)
- Fe (iii) ion (55 Da, Ligand)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8hoy
Q-score: 0.292
Xu Y, Wu Y, Zhang Y, Fan R, Yang Y, Li D, Zhu S, Yang B, Zhang Z, Dong C
Cell Res (2023) 33 pp. 479-482 [ DOI: doi:10.1038/s41422-023-00796-1 Pubmed: 36973539 ]
- Dna polymerase processivity factor component a20 (49 kDa, Protein from Monkeypox virus)
- Dna polymerase (120 kDa, Protein from Monkeypox virus)
- E4r (27 kDa, Protein from Monkeypox virus)
- Monkeypox virus replication holoenzyme f8-a22-e4 complex without dna (191 MDa, Complex from Monkeypox virus)
XBB.1.5.10 RBD in complex with ACE2
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8wtd
Q-score: 0.508
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 [ DOI: doi:10.1371/journal.ppat.1011868 Pubmed: 38117863 ]
- Spike protein s2' (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Rbd in complex with ace2 (Complex)
- Human ace2 (Complex from Homo sapiens)
- Xbb.1.5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (92 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1371/journal.ppat.1011868 Pubmed: 38117863 ]
- Processed angiotensin-converting enzyme 2 (68 kDa, Protein from Homo sapiens)
- Human ace2 (Complex from Homo sapiens)
- Spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (145 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Xbb.1.5.70 spike protein in complex with hace2 (Complex)
Resolution: 3.56 Å
EM Method: Single-particle
Fitted PDBs: 8k0b
Q-score: 0.167
Qin Y, Yu D, Wu D, Dong J, Li WT, Ye C, Cheung KC, Zhang Y, Xu Y, Wang Y, Shi YS, Dang S
Nat Commun (2023) 14 pp. 7265-7265 [ DOI: doi:10.1038/s41467-023-42956-2 Pubmed: 37945568 ]
- Calcium permeable stress-gated cation channel 1 (93 kDa, Protein from Mus musculus)
- Tmem63c (Cell from Mus musculus)
Resolution: 5.47 Å
EM Method: Single-particle
Fitted PDBs: 8wak
Q-score: 0.079
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Rna (847 Da, RNA from synthetic construct)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- Structure of transcribing complex 2 (tc2), the initially transcribing complex with pol ii positioned 2nt downstream of tss (Complex)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Tfiih (Complex from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Alpha-amanitin (Complex from Amanita phalloides)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna (Complex from synthetic construct)
- Template dna (30 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Non-template dna (30 kDa, DNA from synthetic construct)
Resolution: 8.52 Å
EM Method: Single-particle
Fitted PDBs: 8wal
Q-score: 0.084
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (30 kDa, DNA from synthetic construct)
- Tfiia (Complex from Homo sapiens)
- Tfiih (Complex from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Structure of transcribing complex 3 (tc3), the initially transcribing complex with pol ii positioned 3nt downstream of tss (Complex)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Alpha-amanitin (Complex from Amanita phalloides)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna (Complex from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Template dna (30 kDa, DNA from synthetic construct)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rna (1 kDa, RNA from synthetic construct)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)