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- EMDB-7137: PRMT5:MEP50 complex -

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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 50
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

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7137.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 220 pix.
= 220. Å		1 Å/pix.
x 220 pix.
= 220. Å		1 Å/pix.
x 220 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Sample components

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Entire : PRMT5:MEP50

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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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
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
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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