[English] 日本語
Yorodumi
- PDB-6ogn: Crystal structure of mouse protein arginine methyltransferase 7 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ogn
TitleCrystal structure of mouse protein arginine methyltransferase 7 in complex with SGC8158 chemical probe
ComponentsProtein arginine N-methyltransferase 7
KeywordsTRANSFERASE / PRMT7 / SGC8158 / chemical probe / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


type III protein arginine methyltransferase / protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / peptidyl-arginine methylation / protein-arginine omega-N symmetric methyltransferase activity / histone H4R3 methyltransferase activity / RMTs methylate histone arginines / genomic imprinting / protein-arginine N-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity ...type III protein arginine methyltransferase / protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / peptidyl-arginine methylation / protein-arginine omega-N symmetric methyltransferase activity / histone H4R3 methyltransferase activity / RMTs methylate histone arginines / genomic imprinting / protein-arginine N-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / histone methyltransferase activity / ribonucleoprotein complex binding / spliceosomal snRNP assembly / fibrillar center / histone binding / chromatin remodeling / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-MJ7 / Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsHalabelian, L. / Dong, A. / Zeng, H. / Li, Y. / Hutchinson, A. / Seitova, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2020
Title: Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response.
Authors: Szewczyk, M.M. / Ishikawa, Y. / Organ, S. / Sakai, N. / Li, F. / Halabelian, L. / Ackloo, S. / Couzens, A.L. / Eram, M. / Dilworth, D. / Fukushi, H. / Harding, R. / Dela Sena, C.C. / Sugo, T. ...Authors: Szewczyk, M.M. / Ishikawa, Y. / Organ, S. / Sakai, N. / Li, F. / Halabelian, L. / Ackloo, S. / Couzens, A.L. / Eram, M. / Dilworth, D. / Fukushi, H. / Harding, R. / Dela Sena, C.C. / Sugo, T. / Hayashi, K. / McLeod, D. / Zepeda, C. / Aman, A. / Sanchez-Osuna, M. / Bonneil, E. / Takagi, S. / Al-Awar, R. / Tyers, M. / Richard, S. / Takizawa, M. / Gingras, A.C. / Arrowsmith, C.H. / Vedadi, M. / Brown, P.J. / Nara, H. / Barsyte-Lovejoy, D.
History
DepositionApr 3, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionApr 17, 2019ID: 6NPG
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9536
Polymers78,3911
Non-polymers2,5625
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.813, 97.813, 169.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Protein arginine N-methyltransferase 7 / Histone-arginine N-methyltransferase PRMT7 / [Myelin basic protein]-arginine N-methyltransferase PRMT7


Mass: 78391.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt7, Kiaa1933 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q922X9, type III protein arginine methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MJ7 / 5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl)methyl]amino}butyl)-5'-thioadenosine


Mass: 555.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31ClN6O3S
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 647.004 Da / Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 % / Mosaicity: 0.418 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20% PEG3350, 0.04 M citric acid, 0.06 M Bis-Tris propane, pH 6.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2019
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33363 / % possible obs: 99.7 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Rrim(I) all: 0.118 / Χ2: 1.919 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4412.21.17216220.6890.3461.2230.61100
2.44-2.4913.40.98416350.8050.2771.0230.628100
2.49-2.5313.60.82516440.8380.230.8570.673100
2.53-2.5913.90.70216430.8830.1930.7290.715100
2.59-2.6413.80.5716150.9110.1570.5910.815100
2.64-2.713.60.50216530.9310.140.5220.873100
2.7-2.7713.50.41216480.950.1150.4281.019100
2.77-2.8513.40.3416480.9640.0950.3541.159100
2.85-2.9313.20.28816660.9760.0820.31.402100
2.93-3.02130.24216520.9780.0690.2511.68100
3.02-3.1312.70.2116440.980.0610.2192.047100
3.13-3.2612.20.18716620.9870.0550.1962.354100
3.26-3.4110.70.16216540.9870.0510.172.87798.9
3.41-3.5811.50.14316430.990.0440.1493.30498.6
3.58-3.8113.50.13216770.9940.0370.1373.248100
3.81-4.113.60.11616960.9950.0320.1213.37899.9
4.1-4.5213.30.10716830.9940.030.1113.393100
4.52-5.17130.10117180.9950.0280.1053.3299.7
5.17-6.5111.40.09317300.9950.0280.0972.97299.3
6.51-50120.07218300.9860.0220.0752.32997.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4C4A

4c4a


Resolution: 2.4→47.03 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.213 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26122 1632 5 %RANDOM
Rwork0.20849 ---
obs0.2111 31243 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 42 42 4786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134870
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174301
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6346645
X-RAY DIFFRACTIONr_angle_other_deg1.181.5749960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78622.222225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79815725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381526
X-RAY DIFFRACTIONr_chiral_restr0.0550.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9616.9522463
X-RAY DIFFRACTIONr_mcbond_other5.966.952461
X-RAY DIFFRACTIONr_mcangle_it8.27310.43068
X-RAY DIFFRACTIONr_mcangle_other8.27210.4033069
X-RAY DIFFRACTIONr_scbond_it5.8447.1482407
X-RAY DIFFRACTIONr_scbond_other5.8477.152405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.93710.5883575
X-RAY DIFFRACTIONr_long_range_B_refined10.50978.4285033
X-RAY DIFFRACTIONr_long_range_B_other10.51478.4575025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 117 -
Rwork0.327 2250 -
obs--100 %

+
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