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Yorodumi- EMDB-31207: TFIID-based PIC-Mediator holo-complex in fully-assembled state (h... -
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-Basic information
Entry | Database: EMDB / ID: EMD-31207 | |||||||||
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Title | TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) | |||||||||
Map data | TFIID-based PIC-MED holo-complex (deletion of MED1-IDR) in assembled state (hPIC-MED) | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / spermine transport / negative regulation of MHC class I biosynthetic process / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / P-TEFb complex binding / regulation of RNA biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex ...positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / spermine transport / negative regulation of MHC class I biosynthetic process / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / P-TEFb complex binding / regulation of RNA biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / SAGA complex assembly / lateral mesodermal cell differentiation / mammary gland branching involved in thelarche / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / G0 to G1 transition / Cytosolic iron-sulfur cluster assembly / TFIIH-class transcription factor complex binding / nucleotide-excision repair, DNA duplex unwinding / thyroid hormone receptor signaling pathway / negative regulation of protein autoubiquitination / central nervous system myelin formation / transcription factor TFTC complex / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / core mediator complex / RNA polymerase II core complex assembly / negative regulation of MHC class II biosynthetic process / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / regulation of vitamin D receptor signaling pathway / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / SLIK (SAGA-like) complex / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / LBD domain binding / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase I core promoter sequence-specific DNA binding / DNA 5'-3' helicase / hepatocyte differentiation / transcriptional start site selection at RNA polymerase II promoter / ventricular trabecula myocardium morphogenesis / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / transcription factor TFIIF complex / thyroid hormone generation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of response to cytokine stimulus / mediator complex / nuclear retinoic acid receptor binding / maintenance of protein location in nucleus / positive regulation of keratinocyte differentiation / adult heart development / Generic Transcription Pathway / RNA Polymerase III Abortive And Retractive Initiation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.13 Å | |||||||||
Authors | Chen X / Qi Y / Wang X / Wu Z / Yin X / Li J / Liu W / Xu Y | |||||||||
Citation | Journal: Science / Year: 2021 Title: Structures of the human Mediator and Mediator-bound preinitiation complex. Authors: Xizi Chen / Xiaotong Yin / Jiabei Li / Zihan Wu / Yilun Qi / Xinxin Wang / Weida Liu / Yanhui Xu / Abstract: The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26- ...The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31207.map.gz | 228.2 MB | EMDB map data format | |
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Header (meta data) | emd-31207-v30.xml emd-31207.xml | 117.1 KB 117.1 KB | Display Display | EMDB header |
Images | emd_31207.png | 62.2 KB | ||
Others | emd_31207_additional_1.map.gz emd_31207_additional_2.map.gz emd_31207_additional_3.map.gz emd_31207_additional_4.map.gz emd_31207_additional_5.map.gz emd_31207_additional_6.map.gz | 396.8 MB 2.1 MB 397.1 MB 2.3 MB 1.9 MB 397.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31207 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31207 | HTTPS FTP |
-Validation report
Summary document | emd_31207_validation.pdf.gz | 339.2 KB | Display | EMDB validaton report |
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Full document | emd_31207_full_validation.pdf.gz | 338.7 KB | Display | |
Data in XML | emd_31207_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_31207_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31207 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31207 | HTTPS FTP |
-Related structure data
Related structure data | 7encMC 7emfC 7enaC 7enjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31207.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TFIID-based PIC-MED holo-complex (deletion of MED1-IDR) in assembled state (hPIC-MED) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.405 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: TFIID
File | emd_31207_additional_1.map | ||||||||||||
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Annotation | TFIID | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TBP
File | emd_31207_additional_2.map | ||||||||||||
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Annotation | TBP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TFIIH
File | emd_31207_additional_3.map | ||||||||||||
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Annotation | TFIIH | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MED-Head
File | emd_31207_additional_4.map | ||||||||||||
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Annotation | MED-Head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MED-Middle
File | emd_31207_additional_5.map | ||||||||||||
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Annotation | MED-Middle | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MED
File | emd_31207_additional_6.map | ||||||||||||
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Annotation | MED | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TFIID-based PIC-Mediator holo-complex in fully-assembled state (h...
+Supramolecule #1: TFIID-based PIC-Mediator holo-complex in fully-assembled state (h...
+Macromolecule #1: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #2: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #3: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #4: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #5: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #6: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #7: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #8: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #9: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #10: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #11: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #12: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #13: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #14: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #15: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #16: Mediator of RNA polymerase II transcription subunit 26
+Macromolecule #17: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #18: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #19: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #20: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #21: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #22: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #23: CDK-activating kinase assembly factor MAT1
+Macromolecule #24: Cyclin-dependent kinase 7
+Macromolecule #25: Cyclin-H
+Macromolecule #26: General transcription factor IIH subunit 1
+Macromolecule #27: General transcription factor IIH subunit 2
+Macromolecule #28: General transcription factor IIH subunit 3
+Macromolecule #29: General transcription factor IIH subunit 4
+Macromolecule #30: General transcription factor IIH subunit 5
+Macromolecule #31: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #32: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #33: General transcription factor IIE subunit 1
+Macromolecule #34: Transcription initiation factor IIE subunit beta
+Macromolecule #35: Transcription initiation factor TFIID subunit 1
+Macromolecule #36: Transcription initiation factor TFIID subunit 2
+Macromolecule #37: Transcription initiation factor TFIID subunit 4
+Macromolecule #38: Transcription initiation factor TFIID subunit 5
+Macromolecule #39: Transcription initiation factor TFIID subunit 6
+Macromolecule #40: Transcription initiation factor TFIID subunit 7
+Macromolecule #41: Transcription initiation factor TFIID subunit 8
+Macromolecule #42: Transcription initiation factor TFIID subunit 9
+Macromolecule #43: Transcription initiation factor TFIID subunit 10
+Macromolecule #44: Transcription initiation factor TFIID subunit 12
+Macromolecule #45: Transcription initiation factor TFIID subunit 3
+Macromolecule #46: Transcription initiation factor TFIID subunit 11
+Macromolecule #47: Transcription initiation factor TFIID subunit 13
+Macromolecule #48: Transcription initiation factor IIA subunit 2
+Macromolecule #49: TATA-box-binding protein
+Macromolecule #50: TFIIA-a
+Macromolecule #51: Transcription initiation factor IIB
+Macromolecule #52: General transcription factor IIF subunit 2
+Macromolecule #55: RPB1
+Macromolecule #56: DNA-directed RNA polymerase subunit beta
+Macromolecule #57: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #58: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #59: DNA-directed RNA polymerase II subunit E
+Macromolecule #60: DNA-directed RNA polymerase II subunit F
+Macromolecule #61: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #62: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #63: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #64: RPB10
+Macromolecule #65: RNA_pol_L_2 domain-containing protein
+Macromolecule #66: RPB12
+Macromolecule #67: General transcription factor IIF subunit 1
+Macromolecule #68: Mediator of RNA polymerase II transcription subunit 23
+Macromolecule #69: Mediator of RNA polymerase II transcription subunit 24
+Macromolecule #70: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #53: DNA (69-MER)
+Macromolecule #54: DNA (69-MER)
+Macromolecule #71: ZINC ION
+Macromolecule #72: IRON/SULFUR CLUSTER
+Macromolecule #73: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67732 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |