[English] 日本語
Yorodumi
- PDB-5fub: Crystal Structure of zebrafish Protein Arginine Methyltransferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fub
TitleCrystal Structure of zebrafish Protein Arginine Methyltransferase 2 catalytic domain with SAH
ComponentsPROTEIN ARGININE METHYLTRANSFERASE 2
KeywordsTRANSFERASE / S-ADENOSYL-L-CYSTEINE / S-ADENOSYL-L-HOMOCYSTEINE
Function / homology
Function and homology information


peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / identical protein binding / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / SH3 domain / Distorted Sandwich / Src homology 3 domains ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / SH3 domain / Distorted Sandwich / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine methyltransferase 2
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsCura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
CitationJournal: FEBS J. / Year: 2017
Title: Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors.
Authors: Cura, V. / Marechal, N. / Troffer-Charlier, N. / Strub, J.M. / van Haren, M.J. / Martin, N.I. / Cianferani, S. / Bonnefond, L. / Cavarelli, J.
History
DepositionJan 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Structure summary
Revision 1.2Nov 30, 2016Group: Data collection / Database references / Structure summary
Revision 1.3Dec 7, 2016Group: Database references
Revision 1.4Mar 1, 2017Group: Database references
Revision 1.5Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN ARGININE METHYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,28610
Polymers38,3771
Non-polymers9099
Water3,261181
1
A: PROTEIN ARGININE METHYLTRANSFERASE 2
hetero molecules

A: PROTEIN ARGININE METHYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57220
Polymers76,7542
Non-polymers1,81918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6750 Å2
ΔGint-51.2 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.070, 147.070, 127.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein PROTEIN ARGININE METHYLTRANSFERASE 2


Mass: 38376.770 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, UNP RESIDUES 73-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: BIOSCIENCE IRAK293-C16 / Plasmid: PDEST20 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A1L1Q4, EC: 2.1.1.125

-
Non-polymers , 6 types, 190 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCRYSTALLIZED PRMT2 SEQUENCE STARTS AT D73 G72 COMES FROM THE TEV CLEAVAGE SITE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64 % / Description: STARTING MODEL GENERATED BY BALBES
Crystal growpH: 6
Details: 9% PEG 20000, 300MM NACL,100MM MES PH 6.0 AND FOR CRYO IS 10% PEG 20000, 300MM NACL,100MM MES PH 6.0, 15% ETHYLENE GLYCOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2→38.4 Å / Num. obs: 35917 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.997→38.405 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 1810 5 %
Rwork0.1817 --
obs0.1834 35917 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.6 Å2
Refinement stepCycle: LAST / Resolution: 1.997→38.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 57 181 2934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042818
X-RAY DIFFRACTIONf_angle_d0.6033817
X-RAY DIFFRACTIONf_dihedral_angle_d15.9311646
X-RAY DIFFRACTIONf_chiral_restr0.043421
X-RAY DIFFRACTIONf_plane_restr0.003479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.05110.31441220.31362620X-RAY DIFFRACTION100
2.0511-2.11140.29821240.27662627X-RAY DIFFRACTION100
2.1114-2.17960.25611260.26172607X-RAY DIFFRACTION100
2.1796-2.25750.30921720.24452589X-RAY DIFFRACTION100
2.2575-2.34780.26671220.22872597X-RAY DIFFRACTION100
2.3478-2.45470.27211450.22122621X-RAY DIFFRACTION100
2.4547-2.58410.23811380.22012602X-RAY DIFFRACTION100
2.5841-2.74590.25411620.20012593X-RAY DIFFRACTION100
2.7459-2.95790.21351400.18972617X-RAY DIFFRACTION100
2.9579-3.25540.24031550.18912623X-RAY DIFFRACTION100
3.2554-3.72610.21741470.16592634X-RAY DIFFRACTION100
3.7261-4.69320.15681370.1372658X-RAY DIFFRACTION100
4.6932-38.41210.17391200.14842719X-RAY DIFFRACTION99
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)
10.2133-0.0174-0.10070.00630.01160.04250.1638-0.0349-0.1157-0.0885-0.0559-0.0225-0.4040.03550.13280.5684-0.05330.04650.17380.01670.34764.582924.264548.044
20.4269-0.0201-0.08490.15980.02020.04950.2420.1431-0.154-0.162-0.07980.1088-0.4891-0.01370.19480.50220.097400.16030.01310.2715-1.17823.679537.0235
30.1223-0.13820.07390.2947-0.01330.08940.0589-0.08810.1198-0.0941-0.0947-0.0507-0.12610.3264-0.05150.3451-0.26220.05260.5463-0.11060.351329.125217.853462.42
41.0053-0.71790.1360.7131-0.06430.07740.18150.22190.0637-0.2691-0.0646-0.0241-0.41920.49910.13340.5195-0.19960.09330.4371-0.0050.315722.820823.692940.6864
50.31310.00220.11450.2047-0.02060.0410.0335-0.034-0.0488-0.1464-0.0299-0.01790.00540.38540.01920.2674-0.1280.04430.5804-0.06050.298932.899615.618148.5129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 72 THROUGH 109 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 110 THROUGH 221 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 222 THROUGH 273 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 274 THROUGH 350 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 351 THROUGH 375)

+
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