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- PDB-7bo7: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437 -

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Basic information

Entry
Database: PDB / ID: 7bo7
TitleCRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437
Components
  • Methylosome protein 50WD repeat-containing protein 77
  • Protein arginine N-methyltransferase 5
KeywordsTRANSLOCASE / complex inhibitor bound PRMT5 MEP50
Function / homology
Function and homology information


positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / 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 / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / 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 / epithelial cell proliferation involved in prostate gland development / histone arginine N-methyltransferase activity / methylosome / protein-arginine N-methyltransferase activity / methyl-CpG binding / positive regulation of mRNA splicing, via spliceosome / : / endothelial cell activation / histone H3 methyltransferase activity / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / regulation of mitotic nuclear division / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / liver regeneration / methyltransferase activity / 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 / chromatin / regulation of DNA-templated transcription / 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. / WD40 repeat, conserved site ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-U6K / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsBrown, D. / Robinson, C. / Carr, K.H. / Pande, V.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437
Authors: Brown, D. / Robinson, C. / Carr, K.H. / Pande, V.
History
DepositionJan 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Protein arginine N-methyltransferase 5
BBB: Methylosome protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2788
Polymers111,3502
Non-polymers9286
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint2 kcal/mol
Surface area36960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.190, 137.250, 179.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AAABBB

#1: Protein Protein arginine N-methyltransferase 5 / 72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / ...72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / Shk1 kinase-binding protein 1 homolog / SKB1Hs


Mass: 73763.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein Methylosome protein 50 / WD repeat-containing protein 77 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / p44/Mep50


Mass: 37586.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9BQA1

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Non-polymers , 5 types, 58 molecules

#3: Chemical ChemComp-U6K / (2~{R},3~{R},4~{S},5~{R})-2-[(4~{a}~{S},7~{a}~{S})-4-azanyl-1,4,4~{a},7~{a}-tetrahydropyrrolo[2,3-d]pyrimidin-7-yl]-5-(quinolin-7-yloxymethyl)oxolane-3,4-diol


Mass: 397.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350, 150mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 2.83→60.367 Å / Num. obs: 30068 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.992 / Net I/σ(I): 10
Reflection shellResolution: 2.83→2.98 Å / Rmerge(I) obs: 1.379 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4286 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RLQ

6rlq


Resolution: 2.83→60.367 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.169 / SU B: 22.28 / SU ML: 0.382 / Average fsc free: 0.8639 / Average fsc work: 0.825 / Cross valid method: FREE R-VALUE / ESU R Free: 0.365
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.25 1310 4.357 %
Rwork0.205 28757 -
all0.207 --
obs-30067 99.596 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.138 Å2
Baniso -1Baniso -2Baniso -3
1-4.717 Å20 Å20 Å2
2--2.329 Å2-0 Å2
3----7.046 Å2
Refinement stepCycle: LAST / Resolution: 2.83→60.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 63 52 7377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137555
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176899
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.63810307
X-RAY DIFFRACTIONr_angle_other_deg1.2271.57115886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8045930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86422.28386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.955151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9651545
X-RAY DIFFRACTIONr_chiral_restr0.0650.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021753
X-RAY DIFFRACTIONr_nbd_refined0.2060.21458
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.26692
X-RAY DIFFRACTIONr_nbtor_refined0.170.23498
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2176
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.214
X-RAY DIFFRACTIONr_nbd_other0.1860.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2930.24
X-RAY DIFFRACTIONr_mcbond_it5.1156.7753729
X-RAY DIFFRACTIONr_mcbond_other5.1096.7733728
X-RAY DIFFRACTIONr_mcangle_it7.78310.1554656
X-RAY DIFFRACTIONr_mcangle_other7.78210.1574657
X-RAY DIFFRACTIONr_scbond_it4.9527.0673825
X-RAY DIFFRACTIONr_scbond_other4.9527.0683826
X-RAY DIFFRACTIONr_scangle_it7.78310.4765651
X-RAY DIFFRACTIONr_scangle_other7.78310.4775652
X-RAY DIFFRACTIONr_lrange_it11.915127.77630371
X-RAY DIFFRACTIONr_lrange_other11.915127.76930364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.9032900.3932180X-RAY DIFFRACTION98.7766
2.903-2.9830.418320.3752070X-RAY DIFFRACTION97.8585
2.983-3.0690.398810.3181997X-RAY DIFFRACTION99.76
3.069-3.1640.278990.271931X-RAY DIFFRACTION99.8524
3.164-3.2670.311120.2851872X-RAY DIFFRACTION99.9496
3.267-3.3820.294830.2571819X-RAY DIFFRACTION99.9474
3.382-3.510.361770.2351753X-RAY DIFFRACTION99.9454
3.51-3.6530.294840.2221699X-RAY DIFFRACTION99.888
3.653-3.8150.322620.1971630X-RAY DIFFRACTION99.9409
3.815-4.0010.23840.1761546X-RAY DIFFRACTION99.9387
4.001-4.2170.226870.1651462X-RAY DIFFRACTION99.4862
4.217-4.4720.172900.1441367X-RAY DIFFRACTION99.3861
4.472-4.7810.236740.1481323X-RAY DIFFRACTION100
4.781-5.1630.19650.1431235X-RAY DIFFRACTION100
5.163-5.6540.207750.1671135X-RAY DIFFRACTION99.9174
5.654-6.320.236490.1781041X-RAY DIFFRACTION100
6.32-7.2930.23530.171928X-RAY DIFFRACTION99.8982
7.293-8.9220.199390.158777X-RAY DIFFRACTION98.9091
8.922-12.5760.21310.142632X-RAY DIFFRACTION99.8494
12.576-60.3670.337330.277360X-RAY DIFFRACTION98.7437

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