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Yorodumi- EMDB-31204: TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre... -
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-Basic information
Entry | Database: EMDB / ID: EMD-31204 | |||||||||
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Title | TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) | |||||||||
Map data | TFIID-based PIC-MED holo-complex (deletion of MED1-IDR) in pre-assembled state (pre-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 / enucleate erythrocyte development / spermine transport / negative regulation of MHC class I biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition ...positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / spermine transport / negative regulation of MHC class I biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / MMXD complex / retinal pigment epithelium development / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / G0 to G1 transition / TFIIH-class transcription factor complex binding / pre-snoRNP complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / thyroid hormone mediated signaling pathway / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / negative regulation of protein autoubiquitination / transcription factor TFTC complex / positive regulation of mitotic recombination / core mediator complex / regulation of vitamin D receptor signaling pathway / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / hair cell differentiation / negative regulation of MHC class II biosynthetic process / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / SLIK (SAGA-like) complex / UV protection / CAK-ERCC2 complex / transcription factor TFIIK complex / nuclear DNA-directed RNA polymerase complex / RNA polymerase III general transcription initiation factor activity / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / positive regulation of response to cytokine stimulus / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / hepatocyte differentiation / maintenance of protein location in nucleus / 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 III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / thyroid hormone generation / 5'-3' DNA helicase activity / positive regulation of androgen receptor activity / 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 keratinocyte differentiation / Generic Transcription Pathway Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.07 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_31204.map.gz | 277 MB | EMDB map data format | |
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Header (meta data) | emd-31204-v30.xml emd-31204.xml | 133 KB 133 KB | Display Display | EMDB header |
Images | emd_31204.png | 85.4 KB | ||
Others | emd_31204_additional_1.map.gz emd_31204_additional_2.map.gz emd_31204_additional_3.map.gz emd_31204_additional_4.map.gz emd_31204_additional_5.map.gz emd_31204_additional_6.map.gz emd_31204_additional_7.map.gz | 3.7 MB 2.7 MB 3.8 MB 277.8 MB 11.8 MB 397.9 MB 2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31204 | HTTPS FTP |
-Related structure data
Related structure data | 7enaMC 7emfC 7encC 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_31204.map.gz / Format: CCP4 / Size: 512 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 pre-assembled state (pre-hPIC-MED) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3175 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 7.1 Angstrom TFIID
File | emd_31204_additional_1.map | ||||||||||||
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Annotation | 7.1 Angstrom TFIID | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 7.3 Angstrom TFIIH
File | emd_31204_additional_2.map | ||||||||||||
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Annotation | 7.3 Angstrom TFIIH | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 4.0 Angstrom MED
File | emd_31204_additional_3.map | ||||||||||||
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Annotation | 4.0 Angstrom MED | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3.9 Angstrom MED-Head
File | emd_31204_additional_4.map | ||||||||||||
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Annotation | 3.9 Angstrom MED-Head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 6.2 Angstrom MED-Middle
File | emd_31204_additional_5.map | ||||||||||||
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Annotation | 6.2 Angstrom MED-Middle | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 5.7 Angstrom CAK
File | emd_31204_additional_6.map | ||||||||||||
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Annotation | 5.7 Angstrom CAK | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3.7 Angstrom TBP
File | emd_31204_additional_7.map | ||||||||||||
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Annotation | 3.7 Angstrom TBP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre...
+Supramolecule #1: TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre...
+Supramolecule #2: TFIID
+Supramolecule #3: DNA-directed RNA polymerase
+Supramolecule #4: DNA
+Supramolecule #5: TFIIH
+Supramolecule #6: TFIIA
+Supramolecule #7: TFIIB
+Supramolecule #8: TFIIF
+Supramolecule #9: TFIIE
+Supramolecule #10: Mediator
+Macromolecule #1: CDK-activating kinase assembly factor MAT1
+Macromolecule #2: Cyclin-dependent kinase 7
+Macromolecule #3: Cyclin-H
+Macromolecule #4: Transcription initiation factor IIA subunit 2
+Macromolecule #5: TATA-box-binding protein
+Macromolecule #6: TFIIA-a
+Macromolecule #7: Transcription initiation factor IIB
+Macromolecule #8: General transcription factor IIF subunit 1
+Macromolecule #9: General transcription factor IIF subunit 2
+Macromolecule #10: RPB1
+Macromolecule #11: DNA-directed RNA polymerase subunit beta
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #14: DNA-directed RNA polymerase II subunit E
+Macromolecule #15: DNA-directed RNA polymerase II subunit F
+Macromolecule #16: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #17: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #18: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #19: RPB10
+Macromolecule #20: RNA_pol_L_2 domain-containing protein
+Macromolecule #21: RPB12
+Macromolecule #22: Transcription initiation factor TFIID subunit 1
+Macromolecule #23: Transcription initiation factor TFIID subunit 2
+Macromolecule #24: Transcription initiation factor TFIID subunit 4
+Macromolecule #25: Transcription initiation factor TFIID subunit 5
+Macromolecule #26: Transcription initiation factor TFIID subunit 6
+Macromolecule #27: Transcription initiation factor TFIID subunit 7
+Macromolecule #28: Transcription initiation factor TFIID subunit 8
+Macromolecule #29: Transcription initiation factor TFIID subunit 9
+Macromolecule #30: Transcription initiation factor TFIID subunit 10
+Macromolecule #31: Transcription initiation factor TFIID subunit 12
+Macromolecule #32: Transcription initiation factor TFIID subunit 3
+Macromolecule #33: Transcription initiation factor TFIID subunit 11
+Macromolecule #34: Transcription initiation factor TFIID subunit 13
+Macromolecule #35: General transcription factor IIE subunit 1
+Macromolecule #36: Transcription initiation factor IIE subunit beta
+Macromolecule #37: General transcription factor IIH subunit 1
+Macromolecule #38: General transcription factor IIH subunit 2
+Macromolecule #39: General transcription factor IIH subunit 3
+Macromolecule #40: General transcription factor IIH subunit 4
+Macromolecule #41: General transcription factor IIH subunit 5
+Macromolecule #42: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #43: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #44: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #45: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #46: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #47: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #48: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #49: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #50: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #51: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #52: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #53: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #54: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #55: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #56: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #57: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #58: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #59: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #60: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #61: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #62: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #63: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #64: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #65: Mediator of RNA polymerase II transcription subunit 26
+Macromolecule #66: Mediator of RNA polymerase II transcription subunit 24
+Macromolecule #67: Mediator of RNA polymerase II transcription subunit 23
+Macromolecule #68: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #69: DNA (69-MER)
+Macromolecule #70: DNA(69-MER)
+Macromolecule #71: ZINC ION
+Macromolecule #72: MAGNESIUM ION
+Macromolecule #73: IRON/SULFUR CLUSTER
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48654 |