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Yorodumi- EMDB-34360: PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34360 | |||||||||
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Title | PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state | |||||||||
Map data | PIC-Mediator in complex with plus 1 nucleosome (T40N) in H-binding state | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of mediator complex assembly / 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 / regulation of RNA biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex ...positive regulation of mediator complex assembly / 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 / regulation of RNA biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / androgen biosynthetic process / positive regulation of G0 to G1 transition / DNA-templated transcription open complex formation / allantois development / mammary gland branching involved in thelarche / retinal pigment epithelium development / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / TFIIH-class transcription factor complex binding / G0 to G1 transition / thyroid hormone receptor signaling pathway / negative regulation of protein autoubiquitination / central nervous system myelin formation / positive regulation of core promoter binding / transcription factor TFTC complex / RNA polymerase II core complex assembly / core mediator complex / positive regulation of mitotic recombination / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / hair follicle maturation / RNA polymerase transcription factor SL1 complex / ventricular system development / snRNA transcription by RNA polymerase II / hair cell differentiation / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / regulation of vitamin D receptor signaling pathway / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / phosphatase activator activity / nucleotide-excision repair, preincision complex assembly / SLIK (SAGA-like) complex / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / 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 / TFIIF-class transcription factor complex binding / hepatocyte differentiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcriptional start site selection at RNA polymerase II 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 - 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / ventricular trabecula myocardium morphogenesis / positive regulation of response to cytokine stimulus / thyroid hormone generation / transcription factor TFIIF complex / DNA 5'-3' helicase / mediator complex / nuclear retinoic acid receptor binding / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / adult heart development / positive regulation of androgen receptor activity / positive regulation of keratinocyte differentiation / Generic Transcription Pathway Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Xenopus laevis (African clawed frog) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.16 Å | |||||||||
Authors | Chen X / Wang X / Liu W / Ren Y / Qu X / Li J / Yin X | |||||||||
Funding support | 1 items
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Citation | Journal: Science / Year: 2022 Title: Structures of +1 nucleosome-bound PIC-Mediator complex. Authors: Xizi Chen / Xinxin Wang / Weida Liu / Yulei Ren / Xuechun Qu / Jiabei Li / Xiaotong Yin / Yanhui Xu / Abstract: RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream ...RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription. The +1 nucleosome-bound PIC-Mediator structures show that PIC-Mediator prefers binding to T40N nucleosome located 40 base pairs downstream of TSS and contacts T50N but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26 and may contribute to transcription initiation. PIC-Mediator exhibits multiple nucleosome-binding patterns, supporting a structural role of the +1 nucleosome in the coordination of PIC-Mediator assembly. Our study reveals the molecular mechanism of PIC-Mediator organization on chromatin and underscores the significance of the +1 nucleosome in regulating transcription initiation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34360.map.gz | 17.9 MB | EMDB map data format | |
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Header (meta data) | emd-34360-v30.xml emd-34360.xml | 126.5 KB 126.5 KB | Display Display | EMDB header |
Images | emd_34360.png | 59.1 KB | ||
Others | emd_34360_additional_1.map.gz emd_34360_half_map_1.map.gz emd_34360_half_map_2.map.gz | 8.9 MB 261 MB 261 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34360 | HTTPS FTP |
-Validation report
Summary document | emd_34360_validation.pdf.gz | 676.7 KB | Display | EMDB validaton report |
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Full document | emd_34360_full_validation.pdf.gz | 676.3 KB | Display | |
Data in XML | emd_34360_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | emd_34360_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34360 | HTTPS FTP |
-Related structure data
Related structure data | 8gxsMC 8gxqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34360.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | PIC-Mediator in complex with plus 1 nucleosome (T40N) in H-binding state | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_34360_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Nucleosome of the PIC-Mediator in complex with plus...
File | emd_34360_half_map_1.map | ||||||||||||
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Annotation | Nucleosome of the PIC-Mediator in complex with plus 1 nucleosome (T40N) in H-binding state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34360_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
+Supramolecule #1: PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
+Macromolecule #1: DNA (228-mer)
+Macromolecule #2: DNA (228-mer)
+Macromolecule #3: DNA (162-mer)
+Macromolecule #4: DNA (162-mer)
+Macromolecule #5: Transcription initiation factor IIB
+Macromolecule #6: Transcription initiation factor TFIID subunit 1
+Macromolecule #7: General transcription factor IIE subunit 1
+Macromolecule #8: General transcription factor IIF subunit 1
+Macromolecule #9: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #10: Histone H3
+Macromolecule #11: DNA-directed RNA polymerase subunit
+Macromolecule #12: Transcription initiation factor TFIID subunit 2
+Macromolecule #13: Transcription initiation factor IIE subunit beta
+Macromolecule #14: General transcription factor IIF subunit 2
+Macromolecule #15: General transcription factor IIH subunit 1
+Macromolecule #16: Histone H4
+Macromolecule #17: DNA-directed RNA polymerase subunit beta
+Macromolecule #18: General transcription factor IIH subunit 4
+Macromolecule #19: Transcription initiation factor IIA subunit 2
+Macromolecule #20: TATA-box-binding protein
+Macromolecule #21: Transcription initiation factor IIA subunit 1
+Macromolecule #22: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #23: DNA-directed RNA polymerase II subunit E
+Macromolecule #24: DNA-directed RNA polymerase II subunit F
+Macromolecule #25: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #26: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #27: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #28: RNA_pol_L_2 domain-containing protein
+Macromolecule #29: RPB12
+Macromolecule #30: CDK-activating kinase assembly factor MAT1
+Macromolecule #31: General transcription factor IIH subunit 2
+Macromolecule #32: General transcription factor IIH subunit 3
+Macromolecule #33: General transcription factor IIH subunit 5
+Macromolecule #34: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #35: Transcription initiation factor TFIID subunit 4
+Macromolecule #36: Transcription initiation factor TFIID subunit 5
+Macromolecule #37: Transcription initiation factor TFIID subunit 6
+Macromolecule #38: Transcription initiation factor TFIID subunit 7
+Macromolecule #39: Transcription initiation factor TFIID subunit 8
+Macromolecule #40: Transcription initiation factor TFIID subunit 9
+Macromolecule #41: Transcription initiation factor TFIID subunit 12
+Macromolecule #42: Transcription initiation factor TFIID subunit 3
+Macromolecule #43: Transcription initiation factor TFIID subunit 10
+Macromolecule #44: Transcription initiation factor TFIID subunit 11
+Macromolecule #45: Transcription initiation factor TFIID subunit 13
+Macromolecule #46: Cyclin-dependent kinase 7
+Macromolecule #47: Cyclin-H
+Macromolecule #48: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #49: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #50: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #51: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #52: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #53: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #54: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #55: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #56: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #57: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #58: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #59: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #60: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #61: Mediator of RNA polymerase II transcription subunit 26
+Macromolecule #62: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #63: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #64: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #65: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #66: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #67: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #68: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #69: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #70: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #71: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #72: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #73: Mediator of RNA polymerase II transcription subunit 23
+Macromolecule #74: Mediator of RNA polymerase II transcription subunit 24
+Macromolecule #75: Mediator of RNA polymerase II transcription subunit 25
+Macromolecule #76: HISTONE H2A.Z
+Macromolecule #77: Histone H2B
+Macromolecule #78: ZINC ION
+Macromolecule #79: IRON/SULFUR CLUSTER
+Macromolecule #80: 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 K3 (6k 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29473 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |