[English] 日本語
Yorodumi
- EMDB-7137: PRMT5:MEP50 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7137
TitlePRMT5:MEP50 complex
Map dataPRMT5:MEP50 complex
Sample
  • Complex: PRMT5:MEP50
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein 50WD repeat-containing protein 77
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTimm DE
CitationJournal: PLoS One / Year: 2018
Title: Cryo-electron microscopy structure of a human PRMT5:MEP50 complex.
Authors: David E Timm / Valorie Bowman / Russell Madsen / Charles Rauch /
Abstract: Protein arginine methyl transferase 5 (PRMT5) is a signaling protein and histone modifying enzyme that is important in many cellular processes, including regulation of eukaryotic gene transcription. ...Protein arginine methyl transferase 5 (PRMT5) is a signaling protein and histone modifying enzyme that is important in many cellular processes, including regulation of eukaryotic gene transcription. Reported here is a 3.7 Å structure of PRMT5, solved in complex with regulatory binding subunit MEP50 (methylosome associated protein 50, WDR77, p44), by single particle (SP) cryo-Electron Microscopy (cryo-EM) using micrographs of particles that are visibly crowded and aggregated. Despite suboptimal micrograph appearance, this cryo-EM structure is in good agreement with previously reported crystal structures of the complex, which revealed a 450 kDa hetero-octameric assembly having internal D2 symmetry. The catalytic PRMT5 subunits form a core tetramer and the MEP50 subunits are arranged peripherally in complex with the PRMT5 N-terminal domain. The cryo-EM reconstruction shows good side chain definition and shows a well-resolved peak for a bound dehydrosinefungin inhibitor molecule. These results demonstrate the applicability of cryo-EM in determining structures of human protein complexes of biomedical significance and suggests cryo-EM could be further utilized to understand PRMT5 interactions with other biologically important binding proteins and ligands.
History
DepositionDec 4, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 20, 2017-
UpdateJul 3, 2019-
Current statusJul 3, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7137.png

Downloads & links

-
Map

FileDownload / File: emd_7137.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPRMT5:MEP50 complex
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.12176832 - 0.22226366
Average (Standard dev.)0.0007388665 (±0.012074247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.1220.2220.001

-
Supplemental data

-
Sample components

-
Entire : PRMT5:MEP50

EntireName: PRMT5:MEP50
Components
  • Complex: PRMT5:MEP50
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein 50WD repeat-containing protein 77

-
Supramolecule #1: PRMT5:MEP50

SupramoleculeName: PRMT5:MEP50 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The complex contains a tetramer of PRMT5:MEP50 heterodimers
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightExperimental: 450 KDa

-
Macromolecule #1: Protein arginine N-methyltransferase 5

MacromoleculeName: Protein arginine N-methyltransferase 5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRGPNSGTEK GRLVIPEKQG FDFLCMPVFH PRFKREFIQE PAKNRPGPQT RSDLLLSGRA FLLPLNQEDN TNLARVLTN HIHTGHHSSM FWMRVPLVAP EDLRDDIIEN APTTHTEEYS GEEKTWMWWH NFRTLCDYSK R IAVALEIG ADLPSNHVID RWLGEPIKAA ...String:
MRGPNSGTEK GRLVIPEKQG FDFLCMPVFH PRFKREFIQE PAKNRPGPQT RSDLLLSGRA FLLPLNQEDN TNLARVLTN HIHTGHHSSM FWMRVPLVAP EDLRDDIIEN APTTHTEEYS GEEKTWMWWH NFRTLCDYSK R IAVALEIG ADLPSNHVID RWLGEPIKAA ILPTSIFLTN KKGFPVLSKM HQRLIFRLLK LEVQFIITGT NH HSEKEFC SYLQYLEYLS QNRPPPNAYE LFAKGYEDYL QSPLQPLMDN LESQTYEVFE KDPIKYSQYQ QAI YKCLLD RVPEEEKDTN VQVLMVLGAG RGPLVNASLR AAKQADRRIK LYAVEKNPNA VVTLENWQFE EWGS QVTVV SSDMREWVAP EKADIIVSEL LGSFADNELS PECLDGAQHF LKDDGVSIPG EYTSFLAPIS SSKLY NEVR ACREKDRDPE AQFEMPYVVR LHNFHQLSAP QPCFTFSHPN RDPMIDNNRY CTLEFPVEVN TVLHGF AGY FETVLYQDIT LSIRPETHSP GMFSWFPILF PIKQPITVRE GQTICVRFWR CSNSKKVWYE WAVTAPV CS AIHNPTGRSY TIGL

-
Macromolecule #2: Methylosome protein 50

MacromoleculeName: Methylosome protein 50 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRKETPPPLV PPAAREWNLP PNAPACMERQ LEAARYRSDG ALLLGASSLS GRCWAGSLWL FKDPCAAPNE GFCSAGVQT EAGVADLTWV GERGILVASD SAHAAQVTCV AASPHKDSVF LSCSEDNRIL LWDTRCPKPA S QIGCSAPG YLPTSLAWHP QQSEVFVFGD ...String:
MRKETPPPLV PPAAREWNLP PNAPACMERQ LEAARYRSDG ALLLGASSLS GRCWAGSLWL FKDPCAAPNE GFCSAGVQT EAGVADLTWV GERGILVASD SAHAAQVTCV AASPHKDSVF LSCSEDNRIL LWDTRCPKPA S QIGCSAPG YLPTSLAWHP QQSEVFVFGD ENGTVSLVDT KSTSCVLSSA VHSQCVTGLV FSPHSVPFLA SL SEDCSLA VLDSSLSELF RSQAHRDFVR DATWSPLNHS LLTTVGWDHQ VVHHVVPTEP LPAPGPASVT E

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.38 mg/mL
BufferpH: 7.4 / Details: 50 mM HEPES, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 193 / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 113167
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4gqb


Details: low pass filter 60 Ang
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 26553
FSC plot (resolution estimation)

+
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