[English] 日本語
Yorodumi
- PDB-8g2g: Crystal structure of PRMT3 with compound YD1113 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g2g
TitleCrystal structure of PRMT3 with compound YD1113
ComponentsProtein arginine N-methyltransferase 3
KeywordsTRANSFERASE / PRMT3 / YD1113
Function / homology
Function and homology information


protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines ...protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding / methylation / chromatin remodeling / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / Protein arginine N-methyltransferase 3, C2H2 zinc finger domain / Protein arginine N-methyltransferase 3, C2H2 zinc finger / Ribosomal protein L11 methyltransferase (PrmA) / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...: / : / Protein arginine N-methyltransferase 3, C2H2 zinc finger domain / Protein arginine N-methyltransferase 3, C2H2 zinc finger / Ribosomal protein L11 methyltransferase (PrmA) / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-YVU / Protein arginine N-methyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSong, X. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Deng, Y. / Huang, R. / Min, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acta Pharm Sin B / Year: 2023
Title: A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors.
Authors: Deng, Y. / Song, X. / Iyamu, I.D. / Dong, A. / Min, J. / Huang, R.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein arginine N-methyltransferase 3
B: Protein arginine N-methyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6756
Polymers76,5642
Non-polymers1,1114
Water2,936163
1
A: Protein arginine N-methyltransferase 3
hetero molecules

A: Protein arginine N-methyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8678
Polymers76,5642
Non-polymers1,3036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3860 Å2
ΔGint-74 kcal/mol
Surface area25490 Å2
MethodPISA
2
B: Protein arginine N-methyltransferase 3
hetero molecules

B: Protein arginine N-methyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4834
Polymers76,5642
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3490 Å2
ΔGint-32 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.808, 99.863, 170.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Protein arginine N-methyltransferase 3 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 3


Mass: 38281.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT3, HRMT1L3 / Production host: Escherichia coli (E. coli)
References: UniProt: O60678, type I protein arginine methyltransferase
#2: Chemical ChemComp-YVU / 5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine


Mass: 459.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium sulfate

-
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 EIGER2 X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 53430 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.075 / Χ2: 0.997 / Net I/av σ(I): 25.2 / Net I/σ(I): 9.4
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2619 / CC1/2: 0.693 / CC star: 0.905 / Χ2: 0.811 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→47.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.121 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23172 1153 2.2 %RANDOM
Rwork0.19485 ---
obs0.19562 52232 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.889 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å2-0 Å2
2---0.59 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.02→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 74 163 5077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135037
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174610
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.636838
X-RAY DIFFRACTIONr_angle_other_deg1.2791.58510691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02523.839211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43515845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4271512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021014
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_it2.3023.6182505
X-RAY DIFFRACTIONr_mcbond_other2.33.6162503
X-RAY DIFFRACTIONr_mcangle_it3.1625.4093127
X-RAY DIFFRACTIONr_mcangle_other3.1625.4093128
X-RAY DIFFRACTIONr_scbond_it2.9613.9582532
X-RAY DIFFRACTIONr_scbond_other2.9513.9452522
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4775.7893698
X-RAY DIFFRACTIONr_long_range_B_refined5.85442.3235377
X-RAY DIFFRACTIONr_long_range_B_other5.85142.2925356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.024→2.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 84 -
Rwork0.285 3780 -
obs--98.55 %

+
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