[English] 日本語
Yorodumi
- PDB-8rbk: Bos taurus PRMT9 in the presence of SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rbk
TitleBos taurus PRMT9 in the presence of SAH
ComponentsMGC151858 protein
KeywordsTRANSFERASE / METHYLTRANSFERASE / PRMT9 / TPR / SAH
Function / homology
Function and homology information


protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / histone methyltransferase activity / mRNA processing / chromatin remodeling / cytoplasm
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / MGC151858 protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsBonnefond, L. / Cavarelli, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0010-01 France
CitationJournal: To Be Published
Title: Crystal structure of PRMT9 with SAH
Authors: Bonnefond, L. / Cavarelli, J.
History
DepositionDec 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MGC151858 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4882
Polymers93,1031
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, native mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.433, 121.247, 67.355
Angle α, β, γ (deg.)90.00, 113.32, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MGC151858 protein / Protein arginine methyltransferase 9


Mass: 93103.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRMT9, MGC151858 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A5PJT3
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris pH 7.5 0.8 M A.S. 2.5% PEG 6,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980115 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980115 Å / Relative weight: 1
ReflectionResolution: 3.6→45.97 Å / Num. obs: 12994 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Χ2: 1.01 / Net I/σ(I): 8.4 / Num. measured all: 90508
Reflection shellResolution: 3.6→3.94 Å / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 2.446 / Num. measured all: 21045 / Num. unique obs: 3096 / CC1/2: 0.516 / Rpim(I) all: 1.012 / Rrim(I) all: 2.65 / Χ2: 1.08 / Net I/σ(I) obs: 0.8

-
Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→45.97 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 626 4.83 %RANDOM
Rwork0.2389 ---
obs0.2409 12972 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 26 0 5856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025980
X-RAY DIFFRACTIONf_angle_d0.5298113
X-RAY DIFFRACTIONf_dihedral_angle_d7.189796
X-RAY DIFFRACTIONf_chiral_restr0.042932
X-RAY DIFFRACTIONf_plane_restr0.0041030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.960.40781660.35463062X-RAY DIFFRACTION99
3.96-4.530.31091470.27193065X-RAY DIFFRACTION100
4.54-5.710.29351530.2563091X-RAY DIFFRACTION100
5.71-45.970.25211600.21043128X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.9338-1.411-3.97858.4202-0.39325.65650.44920.7751.29530.5207-0.3666-1.1597-0.06870.4465-0.21561.5663-0.0155-0.20741.4706-0.07011.7091-8.9264-30.330724.677
23.38350.1849-1.44373.033-0.5231.1044-0.0682-0.9923-0.23140.56260.1175-0.17920.04620.4001-0.00311.887-0.3027-0.03331.9666-0.01291.824128.93-23.97230.6928
34.07312.330.18852.2544-1.11249.4467-0.75720.26840.2552-0.15780.1051-0.5577-0.3621.80930.83851.254-0.2789-0.13151.2662-0.22761.454644.1311-7.153327.3823
42.87380.67840.93790.56520.31083.6631-0.02970.0480.1996-0.02160.18910.0924-0.7414-0.0217-0.15851.7292-0.27450.20711.5143-0.08611.723124.4801-5.14765.4787
53.2199-0.74160.68462.6086-2.654.7393-0.10270.4546-0.5483-0.1867-0.0578-0.32070.32490.49340.12221.7081-0.25040.05361.4039-0.37161.696830.4901-30.07054.33
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 415 )
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 704 )
5X-RAY DIFFRACTION5chain 'A' and (resid 705 through 846 )

+
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