[English] 日本語
Yorodumi
- EMDB-25197: Cryo-EM structure of 7SK core RNP with linear RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25197
TitleCryo-EM structure of 7SK core RNP with linear RNA
Map data7SK core RNP with linear RNA
Sample
  • Complex: 7SK linear core RNP with MePCE,Larp7 and linear 7SK RNA
    • Complex: 7SK snRNA methylphosphate capping enzyme, La-related protein 7
      • Protein or peptide: 7SK snRNA methylphosphate capping enzyme
      • Protein or peptide: La-related protein 7
    • Complex: RNA
      • RNA: Linear 7SK RNA
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
Keywordsnon-coding RNA / La-related protein / methylphosphate capping enzyme / transcription regulation / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


RNA 5'-gamma-phosphate methyltransferase activity / U6 2'-O-snRNA methylation / snRNA metabolic process / snRNA modification / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of protein localization to Cajal body ...RNA 5'-gamma-phosphate methyltransferase activity / U6 2'-O-snRNA methylation / snRNA metabolic process / snRNA modification / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of protein localization to Cajal body / RNA methyltransferase activity / RNA methylation / negative regulation of viral transcription / S-adenosylmethionine-dependent methyltransferase activity / regulation of mRNA splicing, via spliceosome / O-methyltransferase activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of G1/S transition of mitotic cell cycle / U6 snRNA binding / RNA splicing / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA processing / spermatogenesis / cell differentiation / ribonucleoprotein complex / mRNA binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
LARP7, RNA recognition motif 1 / LARP7, RNA recognition motif 2 / La-related protein 7, La domain / RNA methyltransferase bin3, C-terminal / Bin3-type S-adenosyl-L-methionine binding domain / RNA methyltransferase Bin3-like / Bicoid-interacting protein 3 (Bin3) / Bin3-type S-adenosyl-L-methionine (SAM) domain profile. / RNA binding motif / Lupus La protein ...LARP7, RNA recognition motif 1 / LARP7, RNA recognition motif 2 / La-related protein 7, La domain / RNA methyltransferase bin3, C-terminal / Bin3-type S-adenosyl-L-methionine binding domain / RNA methyltransferase Bin3-like / Bicoid-interacting protein 3 (Bin3) / Bin3-type S-adenosyl-L-methionine (SAM) domain profile. / RNA binding motif / Lupus La protein / La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
La-related protein 7 / 7SK snRNA methylphosphate capping enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYang Y / Liu S
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI155170 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
American Heart Association20POST35210850 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP.
Authors: Yuan Yang / Shiheng Liu / Sylvain Egloff / Catherine D Eichhorn / Tanya Hadjian / James Zhen / Tamás Kiss / Z Hong Zhou / Juli Feigon /
Abstract: 7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is ...7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.
History
DepositionOct 24, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25197.png

Downloads & links

-
Map

FileDownload / File: emd_25197.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation7SK core RNP with linear RNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.13048209 - 0.15125369
Average (Standard dev.)-0.000001340885 (±0.005138106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: 7SK core RNP with linear RNA

Fileemd_25197_additional_1.map
Annotation7SK core RNP with linear RNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 7SK linear core RNP with MePCE,Larp7 and linear 7SK RNA

EntireName: 7SK linear core RNP with MePCE,Larp7 and linear 7SK RNA
Components
  • Complex: 7SK linear core RNP with MePCE,Larp7 and linear 7SK RNA
    • Complex: 7SK snRNA methylphosphate capping enzyme, La-related protein 7
      • Protein or peptide: 7SK snRNA methylphosphate capping enzyme
      • Protein or peptide: La-related protein 7
    • Complex: RNA
      • RNA: Linear 7SK RNA
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

-
Supramolecule #1: 7SK linear core RNP with MePCE,Larp7 and linear 7SK RNA

SupramoleculeName: 7SK linear core RNP with MePCE,Larp7 and linear 7SK RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: 7SK snRNA methylphosphate capping enzyme, La-related protein 7

SupramoleculeName: 7SK snRNA methylphosphate capping enzyme, La-related protein 7
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3

-
Macromolecule #1: 7SK snRNA methylphosphate capping enzyme

MacromoleculeName: 7SK snRNA methylphosphate capping enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.122797 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSP LPAAGFKKQQ RKFQYGNYCK YYGYRNPSCE DGRLRVLKPE WFRGRDVLDL GCNVGHLTLS IACKWGPSR MVGLDIDSRL IHSARQNIRH YLSEELRLPP QTLEGDPGAE GEEGTTTVRK RSCFPASLTA SRGPIAAPQV P LDGADTSV ...String:
MGSSHHHHHH SSGLVPRGSP LPAAGFKKQQ RKFQYGNYCK YYGYRNPSCE DGRLRVLKPE WFRGRDVLDL GCNVGHLTLS IACKWGPSR MVGLDIDSRL IHSARQNIRH YLSEELRLPP QTLEGDPGAE GEEGTTTVRK RSCFPASLTA SRGPIAAPQV P LDGADTSV FPNNVVFVTG NYVLDRDDLV EAQTPEYDVV LCLSLTKWVH LNWGDEGLKR MFRRIYRHLR PGGILVLEPQ PW SSYGKRK TLTETIYKNY YRIQLKPEQF SSYLTSPDVG FSSYELVATP HNTSKGFQRP VYLFHKARSP SH

UniProtKB: 7SK snRNA methylphosphate capping enzyme

-
Macromolecule #2: La-related protein 7

MacromoleculeName: La-related protein 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.109129 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GMETESGNQE KVMEEESTEK KKEVEKKKRS RVKQVLADIA KQVDFWFGDA NLHKDRFLRE QIEKSRDGYV DISLLVSFNK MKKLTTDGK LIARALRSSA VVELDLEGTR IRRKKPLGER PKDEDERTVY VELLPKNVNH SWIERVFGKC GNVVYISIPH Y KSTGDPKG ...String:
GMETESGNQE KVMEEESTEK KKEVEKKKRS RVKQVLADIA KQVDFWFGDA NLHKDRFLRE QIEKSRDGYV DISLLVSFNK MKKLTTDGK LIARALRSSA VVELDLEGTR IRRKKPLGER PKDEDERTVY VELLPKNVNH SWIERVFGKC GNVVYISIPH Y KSTGDPKG FAFVEFETKE QAAKAIEFLN NPPEEAPRKP GIFPKTVKNK PIPALRVVEE KKKKKKKKGR MKKEDNIQAK EE NMDTSNT SISKMKRSRP TSEGSDIEST GEEVIPLRVL SKSEWMDLKK EYLALQKASM ASLKKTISQI KSESEMETDS GVP QNTGMK NEKTANREEC RTQEKVNATG PQFVSGVIVK IISTEPLPGR KQVRDTLAAI SEVLYVDLLE GDTECHARFK TPED AQAVI NAYTEINKKH CWKLEILSGD HEQRYWQKIL VDRQAKLNQP REKKRGTEKL ITKAEKIRLA KTQQASKHIR FSEYD

UniProtKB: La-related protein 7, La-related protein 7

-
Macromolecule #3: Linear 7SK RNA

MacromoleculeName: Linear 7SK RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.09623 KDa
SequenceString:
(G5J)GAUGUGAGG GCGACUUCGG UCCUCCCUCA CCGCUCCAUG UGCGAAAUGA GGCGCUGCAU GUGGCAGUCU GCCUUU CUU UU

-
Macromolecule #4: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 159349
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more