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- EMDB-20764: Cryo-EM structure of the apo form of human PRMT5:MEP50 complex at... -

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Basic information

Entry
Database: EMDB / ID: EMD-20764
TitleCryo-EM structure of the apo form of human PRMT5:MEP50 complex at a resolution of 3.4 angstrom.
Map datahandedness corrected, post-processed map of the apo form of human PRMT5:MEP50 complex at 3.4 angstrom
Sample
  • Complex: apo PRMT5:MEP50 complex
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein 50
KeywordsPRMT5 / methyltransferase / TRANSFERASE
Function / homology
Function and homology information


positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / peptidyl-arginine methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / peptidyl-arginine methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / regulation of mitotic nuclear division / histone methyltransferase complex / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / liver regeneration / DNA-templated transcription termination / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. ...: / Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou W / Yadav GP / Jiang Q-X / Li C
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HSSN261200800001E United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA212403 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R21GM131231 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM111367 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM093271 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U24GM116788 United States
CitationJournal: To Be Published
Title: A 3.4-angstrom cryo-EM structure of the apo form of hu-man PRMT5:MEP50 complex reveals sequential catalysis of symmetric methyl transfer
Authors: Zhou W / Yadav GP / Jiang Q-X / Li C
History
DepositionSep 26, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseDec 9, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00597
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00597
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ugh
  • Surface level: 0.00597
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ugh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20764.png

Downloads & links

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Map

FileDownload / File: emd_20764.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhandedness corrected, post-processed map of the apo form of human PRMT5:MEP50 complex at 3.4 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00597 / Movie #1: 0.00597
Minimum - Maximum-0.030123571 - 0.047572255
Average (Standard dev.)0.00012333778 (±0.0014066219)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.660.660.66
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z253.440253.440253.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0300.0480.000

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Supplemental data

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Mask #1

Fileemd_20764_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post-processed map (handedness not corrected)

Fileemd_20764_additional_1.map
Annotationpost-processed map (handedness not corrected)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : apo PRMT5:MEP50 complex

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

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Supramolecule #1: apo PRMT5:MEP50 complex

SupramoleculeName: apo PRMT5:MEP50 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: the apo form of PRMT5:MEP50 heterooctomeric complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 445 KDa

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Macromolecule #1: Protein arginine N-methyltransferase 5

MacromoleculeName: Protein arginine N-methyltransferase 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: type II protein arginine methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.28125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG RATMAAMAVG GAGGSRVSSG RDLNCVPEIA DTLGAVAKQG FDFLCMPVFH PRFKREFIQE PAKNRPGPQT RSDLLLSGR DWNTLIVGKL SPWIRPDSKV EKIRRNSEAA MLQELNFGAY LGLPAFLLPL NQEDNTNLAR VLTNHIHTGH H SSMFWMRV ...String:
MDYKDDDDKG RATMAAMAVG GAGGSRVSSG RDLNCVPEIA DTLGAVAKQG FDFLCMPVFH PRFKREFIQE PAKNRPGPQT RSDLLLSGR DWNTLIVGKL SPWIRPDSKV EKIRRNSEAA MLQELNFGAY LGLPAFLLPL NQEDNTNLAR VLTNHIHTGH H SSMFWMRV PLVAPEDLRD DIIENAPTTH TEEYSGEEKT WMWWHNFRTL CDYSKRIAVA LEIGADLPSN HVIDRWLGEP IK AAILPTS IFLTNKKGFP VLSKMHQRLI FRLLKLEVQF IITGTNHHSE KEFCSYLQYL EYLSQNRPPP NAYELFAKGY EDY LQSPLQ PLMDNLESQT YEVFEKDPIK YSQYQQAIYK CLLDRVPEEE KDTNVQVLMV LGAGRGPLVN ASLRAAKQAD RRIK LYAVE KNPNAVVTLE NWQFEEWGSQ VTVVSSDMRE WVAPEKADII VSELLGSFAD NELSPECLDG AQHFLKDDGV SIPGE YTSF LAPISSSKLY NEVRACREKD RDPEAQFEMP YVVRLHNFHQ LSAPQPCFTF SHPNRDPMID NNRYCTLEFP VEVNTV LHG FAGYFETVLY QDITLSIRPE THSPGMFSWF PILFPIKQPI TVREGQTICV RFWRCSNSKK VWYEWAVTAP VCSAIHN PT GRSYTIGL

UniProtKB: Protein arginine N-methyltransferase 5

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Macromolecule #2: Methylosome protein 50

MacromoleculeName: Methylosome protein 50 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.00366 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMGSRK ETPPPLVPPA AREWNLPPNA PACMERQLEA ARYRSDGALL LGASSLSGRC WAGSLWLFK DPCAAPNEGF CSAGVQTEAG VADLTWVGER GILVASDSGA VELWELDENE TLIVSKFCKY EHDDIVSTVS V LSSGTQAV ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMGSRK ETPPPLVPPA AREWNLPPNA PACMERQLEA ARYRSDGALL LGASSLSGRC WAGSLWLFK DPCAAPNEGF CSAGVQTEAG VADLTWVGER GILVASDSGA VELWELDENE TLIVSKFCKY EHDDIVSTVS V LSSGTQAV SGSKDICIKV WDLAQQVVLS SYRAHAAQVT CVAASPHKDS VFLSCSEDNR ILLWDTRCPK PASQIGCSAP GY LPTSLAW HPQQSEVFVF GDENGTVSLV DTKSTSCVLS SAVHSQCVTG LVFSPHSVPF LASLSEDCSL AVLDSSLSEL FRS QAHRDF VRDATWSPLN HSLLTTVGWD HQVVHHVVPT EPLPAPGPAS VTE

UniProtKB: Methylosome protein WDR77

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.33 %C3H8O3glycerol
2.0 mMC4H10O2S2Dithiothreitol
1.0 %C2H6OSDimethyl sulfoxide
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.0 K / Max: 123.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-39 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 113466
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ckc


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6ugh:
Cryo-EM structure of the apo form of human PRMT5:MEP50 complex at a resolution of 3.4 angstrom

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