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Yorodumi- PDB-7lbm: Structure of the human Mediator-bound transcription pre-initiatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lbm | ||||||||||||||||||
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Title | Structure of the human Mediator-bound transcription pre-initiation complex | ||||||||||||||||||
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Keywords | TRANSCRIPTION/DNA / pre-initiation complex / Mediator / initiation / complex / transcription / TRANSCRIPTION-DNA complex | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of mediator complex assembly / positive regulation of T cell extravasation / LRR domain binding / negative regulation of smooth muscle cell differentiation / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / LRR domain binding / negative regulation of smooth muscle cell differentiation / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / regulation of transcription by RNA polymerase I / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / core mediator complex / hair follicle maturation / ventricular system development / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / RPAP3/R2TP/prefoldin-like complex / RNA polymerase transcription factor SL1 complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / 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 / TFIIF-class transcription factor complex binding / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / DNA 5'-3' helicase / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / mediator complex / RNA Polymerase III Abortive And Retractive Initiation / nuclear retinoic acid receptor binding / G protein-coupled receptor internalization / adult heart development / Generic Transcription Pathway / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / DNA 3'-5' helicase / positive regulation of chromatin binding / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / [RNA-polymerase]-subunit kinase / limb development / transcription preinitiation complex / MicroRNA (miRNA) biogenesis / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / cyclin-dependent protein serine/threonine kinase regulator activity / Viral Messenger RNA Synthesis / regulation of mitotic cell cycle phase transition / Signaling by FGFR2 IIIa TM / hematopoietic stem cell proliferation / cortical actin cytoskeleton / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / termination of RNA polymerase II transcription / RNA polymerase II general transcription initiation factor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / cell division site / spinal cord development / RSV-host interactions / protein acetylation / bone mineralization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / erythrocyte maturation Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||||||||
Authors | Abdella, R. / Talyzina, A. / He, Y. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Science / Year: 2021 Title: Structure of the human Mediator-bound transcription preinitiation complex. Authors: R Abdella / A Talyzina / S Chen / C J Inouye / R Tjian / Y He / Abstract: Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is ...Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lbm.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7lbm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7lbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lbm_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7lbm_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7lbm_validation.xml.gz | 351.7 KB | Display | |
Data in CIF | 7lbm_validation.cif.gz | 563.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/7lbm ftp://data.pdbj.org/pub/pdb/validation_reports/lb/7lbm | HTTPS FTP |
-Related structure data
Related structure data | 23255MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 6 types, 6 molecules 0PQdef
+Mediator of RNA polymerase II transcription subunit ... , 23 types, 23 molecules 123ghijklmnopqrstuvwxyz
+DNA-directed RNA polymerase II subunit ... , 8 types, 8 molecules ABCDEGIK
+DNA-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules FHJL
+Transcription initiation factor ... , 4 types, 4 molecules MNOR
+General transcription factor IIF subunit ... , 2 types, 2 molecules ST
+Super core promoter ... , 2 types, 2 molecules UV
+TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules WX
+General transcription factor IIH subunit ... , 5 types, 5 molecules YZabc
+Non-polymers , 3 types, 19 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 31.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156383 / Symmetry type: POINT |