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- PDB-5fub: Crystal Structure of zebrafish Protein Arginine Methyltransferase... -

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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


type I protein arginine methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / antiviral innate immune response / methylation / chromatin remodeling / regulation of DNA-templated transcription / identical protein binding / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / SH3 domain ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / 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 N-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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Non-polymers , 6 types, 190 molecules

#2: Chemical ChemComp-SAH / 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


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


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


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


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

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Details

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

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Experimental details

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Experiment

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

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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

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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

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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)

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