[English] 日本語
Yorodumi
- PDB-6pdm: Crystal structure of Human Protein Arginine Methyltransferase 9 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pdm
TitleCrystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)
ComponentsProtein arginine N-methyltransferase 9
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / mRNA processing / methylation / chromatin remodeling / regulation of DNA-templated transcription / nucleus / 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 region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHalabelian, L. / Tempel, W. / Zeng, H. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)
Authors: Halabelian, L. / Tempel, W. / Zeng, H. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionJun 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein arginine N-methyltransferase 9


Theoretical massNumber of molelcules
Total (without water)80,48614
Polymers80,4861
Non-polymers013
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.812, 83.802, 65.711
Angle α, β, γ (deg.)90.000, 98.160, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein arginine N-methyltransferase 9 / Protein arginine N-methyltransferase 10


Mass: 80486.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT9, PRMT10 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6P2P2, type II protein arginine methyltransferase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M ammonium nitrate

-
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 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→65.05 Å / Num. obs: 27005 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 69.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 11 / Num. measured all: 92810
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.493.61.208972827040.4680.7391.4190.994.7
8.97-65.053.40.02218465510.9990.0140.02645.599.6

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHENIX.MR_ROSETTA with PDB entry 4C4A

4c4a


Resolution: 2.45→65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.256 / Details: geometry restrained to PHENIX.ROSETTA_REFINE model
RfactorNum. reflection% reflection
Rfree0.26 1310 5.15 %
Rwork0.216 --
obs0.219 25460 99 %
Displacement parametersBiso max: 133.49 Å2 / Biso mean: 66.62 Å2 / Biso min: 42.41 Å2
Baniso -1Baniso -2Baniso -3
1--3.478 Å20 Å213.2393 Å2
2---2.1813 Å20 Å2
3---5.6593 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.45→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 13 0 4482
Biso mean--58.93 --
Num. residues----614
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1849SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1342HARMONIC5
X-RAY DIFFRACTIONt_it8784HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion652SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9510SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8784HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15886HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion12.63
LS refinement shellResolution: 2.45→2.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.234 148 5.15 %
Rwork0.206 2728 -
all0.208 2876 -
obs--99.34 %

+
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