Electron Microscopy Data Bank

EMD-38164

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E3 subunit of the pyruvate dehydrogenase complex

Release date: Nov. 6, 2024
Resolution: 10.2 Å
EM Method: Subtomogram averaging

Chen M, Song Y, Zhang S, Zhang Y, Chen X, Zhang M, Han M, Gao X, Li S, Yang M

Protein Cell (2025) 16 pp. 72-78 [ Pubmed: 39180277 DOI: doi:10.1093/procel/pwae044 ]

Sample:

Native pyruvate dehydrogenase complex (Complex from Sus scrofa)

EMD-37966

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E1 of 2-oxoglutarate dehydrogenase complex subtomogram averaging map

Release date: Oct. 30, 2024
Resolution: 9.7 Å
EM Method: Subtomogram averaging

Zhang Y, Chen M, Chen X, Zhang M, Yin J, Yang Z, Gao X, Zhang S, Yang M

Nat Commun (2024) 15 pp. 8407-8407 [ Pubmed: 39333186 DOI: doi:10.1038/s41467-024-52792-7 ]

Sample:

Mitochondrial complex e1o subunit (Complex from Sus scrofa)

EMD-42063

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I1 symmetry applied adeno-associated virus-9 with human Interleukin 3

Release date: Sept. 18, 2024
Resolution: 11.0 Å
EM Method: Subtomogram averaging

Shay TF, Jang S, Brittain TJ, Chen X, Walker B, Tebbutt C, Fan Y, Wolfe DA, Arokiaraj CM, Sullivan EE, Ding X, Wang TY, Lei Y, Chuapoco MR, Chou TF, Gradinaru V

Nat Commun (2024) 15 pp. 7853-7853 [ DOI: doi:10.1038/s41467-024-52149-0 Pubmed: 39245720 ]

Sample:

Adeno-associated virus-9 and human interleukin 3 complex (46 kDa, Complex from Adeno-associated virus 9)

EMD-37396

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Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS.

Release date: Dec. 6, 2023
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 [ DOI: doi:10.1126/science.adi5120 Pubmed: 38127763 ]

Sample:

General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
Rna polymerase ii (Complex from Sus scrofa)
Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
Rna (Complex from synthetic construct)
Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
Non-template dna (30 kDa, DNA from synthetic construct)
Tfiif (Complex from Homo sapiens)
Dna (Complex from synthetic construct)
Tfiib (Complex from Homo sapiens)
Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
Rpb12 (7 kDa, Protein from Sus scrofa)
Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
Tfiia (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
Alpha-amanitin (Complex from Amanita phalloides)
Tfiid (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
Tfiih (Complex from Homo sapiens)
Tfiie (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
Structure of transcribing complex 3 (tc3), the initially transcribing complex with pol ii positioned 3nt downstream of tss (Complex)
General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
Alpha-amanitin (939 Da, Protein from Amanita phalloides)
Template dna (30 kDa, DNA from synthetic construct)
Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
Iron/sulfur cluster (351 Da, Ligand)
Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
Transcription initiation factor iia subunit 2 (12 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)
Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Rna (1 kDa, RNA from synthetic construct)

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EMD-37412

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De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS

Release date: Dec. 6, 2023
Resolution: 11.47 Å
EM Method: Single-particle

Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y

Science (2023) 382 pp. eadi5120-eadi5120 [ DOI: doi:10.1126/science.adi5120 Pubmed: 38127763 ]

Sample:

Dna (Complex from synthetic construct)
Alpha-amanitin (Complex from Amanita phalloides)
Tfiid (Complex from Homo sapiens)
Rna polymerase ii (Complex from Sus scrofa)
Tfiih (Complex from Homo sapiens)
Tfiie (Complex from Homo sapiens)
Rna (Complex from synthetic construct)
Tfiif (Complex from Homo sapiens)
Tfiib (Complex from Homo sapiens)
Tfiia (Complex from Homo sapiens)
De novo transcribing complex 9 (adml9g), the initially transcribing complex with pol ii positioned 9nt downstream of tss (Complex)

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EMD-33867

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PIC-Mediator (MED26-mut) in complex with +1 nucleosome (T40N)

Release date: Oct. 12, 2022
Resolution: 11.58 Å
EM Method: Single-particle

Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y

Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]

Sample:

Pic-mediator (med26mut) in complex with +1 nucleosome (t40n) (Complex from Sus scrofa)

EMD-34215

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PIC-Mediator in complex with +1 nucleosome (T50N)

Release date: Oct. 12, 2022
Resolution: 9.12 Å
EM Method: Single-particle

Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y

Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]

Sample:

Pic, mediator, transcription initiation, +1 nucleosome (Complex from Sus scrofa)

EMD-34255

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PIC-Mediator (p52-mut) in complex with +1 nucleosome (T40N)

Release date: Oct. 12, 2022
Resolution: 9.9 Å
EM Method: Single-particle

Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y

Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]

Sample:

Pic-mediator (p52-mut) in complex with +1 nucleosome (t40n) (Complex from Sus scrofa)

EMD-34256

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PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)

Release date: Oct. 12, 2022
Resolution: 10.84 Å
EM Method: Single-particle

Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y

Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]

Sample:

Pic-mediator in complex with +1 h2a-containing nucleosome (t40n) (Complex from Sus scrofa)

EMD-31114

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TFIID in canonical conformation

Release date: May 12, 2021
Resolution: 9.0 Å
EM Method: Single-particle
Fitted PDBs: 7ege
Q-score: 0.078

Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y

Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]

Sample:

Tfiid in canonical conformation (Complex from Homo sapiens)
Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)

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