[English] 日本語
Yorodumi
- PDB-4ikp: Crystal structure of coactivator-associated arginine methyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ikp
TitleCrystal structure of coactivator-associated arginine methyltransferase 1 with methylenesinefungin
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / RMTs methylate histone arginines / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-4IK / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, A. / Dombrovski, L. / He, H. / Ibanez, G. / Wernimont, A. / Zheng, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. ...Dong, A. / Dombrovski, L. / He, H. / Ibanez, G. / Wernimont, A. / Zheng, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Luo, M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Elife / Year: 2019
Title: A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion.
Authors: Cai, X.C. / Zhang, T. / Kim, E.J. / Jiang, M. / Wang, K. / Wang, J. / Chen, S. / Zhang, N. / Wu, H. / Li, F. / Dela Sena, C.C. / Zeng, H. / Vivcharuk, V. / Niu, X. / Zheng, W. / Lee, J.P. / ...Authors: Cai, X.C. / Zhang, T. / Kim, E.J. / Jiang, M. / Wang, K. / Wang, J. / Chen, S. / Zhang, N. / Wu, H. / Li, F. / Dela Sena, C.C. / Zeng, H. / Vivcharuk, V. / Niu, X. / Zheng, W. / Lee, J.P. / Chen, Y. / Barsyte, D. / Szewczyk, M. / Hajian, T. / Ibanez, G. / Dong, A. / Dombrovski, L. / Zhang, Z. / Deng, H. / Min, J. / Arrowsmith, C.H. / Mazutis, L. / Shi, L. / Vedadi, M. / Brown, P.J. / Xiang, J. / Qin, L.X. / Xu, W. / Luo, M.
History
DepositionDec 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity_src_gen / struct
Item: _citation.title / _entity_src_gen.host_org_common_name ..._citation.title / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.plasmid_name / _struct.title
Revision 1.3Apr 18, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,02753
Polymers154,9854
Non-polymers2,04249
Water13,385743
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37530
Polymers77,4922
Non-polymers88328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-23 kcal/mol
Surface area26290 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,65223
Polymers77,4922
Non-polymers1,15921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-23 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 98.844, 206.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

#1: Protein
Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4


Mass: 38746.148 Da / Num. of mol.: 4 / Fragment: UNP residues 140-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86X55, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical
ChemComp-4IK / (2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid


Type: L-peptide linking / Mass: 395.414 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N7O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 40 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M Di-AMMONIUM TARTRATE, vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03321 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 104330 / Num. obs: 104330 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.308 / Net I/σ(I): 30.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.036.50.5850550.784198.1
2.03-2.077.20.56251440.811199.5
2.07-2.117.70.49351600.8181100
2.11-2.158.10.45851650.8481100
2.15-2.28.30.38551610.8681100
2.2-2.258.30.33451500.9121100
2.25-2.318.40.29951600.9071100
2.31-2.378.40.26451840.9141100
2.37-2.448.40.2351970.951100
2.44-2.528.40.21151780.9841100
2.52-2.618.40.17852051.0911100
2.61-2.718.40.15352061.2611100
2.71-2.848.40.1351931.3761100
2.84-2.998.40.10752171.3831100
2.99-3.178.30.08552371.5061100
3.17-3.428.30.06852511.7761100
3.42-3.768.20.06652792.4751100
3.76-4.318.20.05452822.4781100
4.31-5.438.20.043535821100
5.43-507.70.03955481.738199.2

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V74

2v74


Resolution: 2→48.11 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2194 / WRfactor Rwork: 0.1915 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8143 / SU B: 4.644 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1886 / SU Rfree: 0.1579 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2080 2 %RANDOM
Rwork0.2034 ---
all0.204 103958 --
obs0.204 103958 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.38 Å2 / Biso mean: 33.9257 Å2 / Biso min: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å2-0 Å2
2---0.29 Å20 Å2
3----2.72 Å2
Refinement stepCycle: LAST / Resolution: 2→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10525 0 182 743 11450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911233
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.95415313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78251402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19424.102512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.727151783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0781545
X-RAY DIFFRACTIONr_chiral_restr0.0770.21701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218610
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 147 -
Rwork0.281 7084 -
all-7231 -
obs--95.16 %

+
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