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- PDB-4c4a: Crystal structure of mouse protein arginine methyltransferase 7 i... -

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Basic information

Entry
Database: PDB / ID: 4c4a
TitleCrystal structure of mouse protein arginine methyltransferase 7 in complex with SAH
ComponentsPROTEIN ARGININE N-METHYLTRANSFERASE 7
KeywordsTRANSFERASE
Function / homology
Function and homology information


type III protein arginine methyltransferase / histone H4 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / RMTs methylate histone arginines / genomic imprinting / S-adenosylmethionine-dependent methyltransferase activity / histone H4R3 methyltransferase activity / spliceosomal snRNP assembly ...type III protein arginine methyltransferase / histone H4 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / RMTs methylate histone arginines / genomic imprinting / S-adenosylmethionine-dependent methyltransferase activity / histone H4R3 methyltransferase activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / fibrillar center / histone binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich ...Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCura, V. / Troffer-Charlier, N. / Bonnefond, L. / Wurtz, J.M. / Cavarelli, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural Insight Into Arginine Methylation by the Mouse Protein Arginine Methyltransferase 7: A Zinc Finger Freezes the Mimic of the Dimeric State Into a Single Active Site.
Authors: Cura, V. / Troffer-Charlier, N. / Wurtz, J.M. / Bonnefond, L. / Cavarelli, J.
History
DepositionSep 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references / Structure summary
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 N-METHYLTRANSFERASE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2185
Polymers78,3911
Non-polymers8274
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.322, 97.322, 168.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN ARGININE N-METHYLTRANSFERASE 7 / HISTONE-ARGININE N-METHYLTRANSFERASE PRMT7 / MYELIN BASIC PROTEIN-ARGININE N-METHYLTRANSFERASE PRMT7


Mass: 78391.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: GENE FROM PLASMID DATABASE MMCD00312554 IMAGE ID 3583763 ORIGINAL CLONE ID MGC-7929 GI 13879452 GENBANK ACCESSION BC006705
Source: (natural) MUS MUSCULUS (house mouse)
References: UniProt: Q922X9, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125, EC: 2.1.1.126

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Non-polymers , 5 types, 696 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-DMX / 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE


Mass: 257.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3S
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.35 % / Description: NONE
Crystal growpH: 7
Details: PEG 20,000 3.2%, PEG 8,000 12.6%, BTP PH 7.0 100 MM, SAH 1 MM, NDSB256 100 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 107019 / % possible obs: 99.9 % / Observed criterion σ(I): 0.5 / Redundancy: 8.7 % / Biso Wilson estimate: 28.86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 0.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAME STRUCTURE SOLVED BY SAD USING A CRYSTAL OF THE NATIVE PROTEIN SOAKED WITH THIMEROSAL AND PHASED WITH ANOMALOUS SIGNAL FROM MERCURY

Resolution: 1.7→29.353 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 4438 5 %
Rwork0.1597 --
obs0.1612 89408 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→29.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 52 692 5837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075334
X-RAY DIFFRACTIONf_angle_d1.1317265
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821974
X-RAY DIFFRACTIONf_chiral_restr0.045795
X-RAY DIFFRACTIONf_plane_restr0.005935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.35231360.32512792X-RAY DIFFRACTION100
1.7193-1.73950.3241510.31592813X-RAY DIFFRACTION100
1.7395-1.76080.3331400.29162757X-RAY DIFFRACTION100
1.7608-1.7830.3041300.27162825X-RAY DIFFRACTION100
1.783-1.80650.29121410.25382785X-RAY DIFFRACTION100
1.8065-1.83120.26451220.22162834X-RAY DIFFRACTION100
1.8312-1.85740.25221670.21742779X-RAY DIFFRACTION100
1.8574-1.88510.22711600.20012785X-RAY DIFFRACTION100
1.8851-1.91460.22951460.19082797X-RAY DIFFRACTION100
1.9146-1.9460.23271440.18532812X-RAY DIFFRACTION100
1.946-1.97950.20751470.18292803X-RAY DIFFRACTION100
1.9795-2.01550.22161560.18262788X-RAY DIFFRACTION100
2.0155-2.05420.20071450.17192840X-RAY DIFFRACTION100
2.0542-2.09620.1931460.16922786X-RAY DIFFRACTION100
2.0962-2.14170.2191480.15922821X-RAY DIFFRACTION100
2.1417-2.19150.2171490.16242791X-RAY DIFFRACTION100
2.1915-2.24630.1841470.15362815X-RAY DIFFRACTION100
2.2463-2.3070.19141500.15282842X-RAY DIFFRACTION100
2.307-2.37490.17031490.15642859X-RAY DIFFRACTION100
2.3749-2.45150.19661460.15662801X-RAY DIFFRACTION100
2.4515-2.53910.21181470.16462815X-RAY DIFFRACTION100
2.5391-2.64070.23711500.16422862X-RAY DIFFRACTION100
2.6407-2.76080.19621530.16412825X-RAY DIFFRACTION100
2.7608-2.90620.1811520.16262855X-RAY DIFFRACTION100
2.9062-3.08810.18071460.15552850X-RAY DIFFRACTION100
3.0881-3.32620.19521500.1652870X-RAY DIFFRACTION100
3.3262-3.66040.17181520.14112868X-RAY DIFFRACTION99
3.6604-4.18880.16381530.13842917X-RAY DIFFRACTION100
4.1888-5.27240.13731530.12252912X-RAY DIFFRACTION99
5.2724-29.35690.17581620.15643071X-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)
11.44610.17660.2211.4590.21321.432-0.0015-0.07250.04670.0463-0.01460.08510.0192-0.1374-0.00090.2087-0.0183-0.01910.20340.01220.207340.041411.34171.9408
21.1950.10651.29960.6552-0.13752.9245-0.00470.03780.08730.0002-0.0661-0.1031-0.19030.15220.06530.1937-0.0072-0.01160.18130.00090.196240.820220.070756.8897
32.48-0.77350.18013.4168-0.05681.40410.08860.29860.1447-0.4888-0.0662-0.1142-0.1082-0.16240.02860.33520.0514-0.01520.2880.00420.211312.440531.073337.6388
40.8538-0.25020.6260.9062-0.05291.68390.0270.1030.0593-0.1016-0.0885-0.0385-0.06620.10780.06750.22120.0230.00730.22860.00560.196434.501218.875944.2095
50.8893-0.2662-0.13092.222-0.00490.71040.02360.0399-0.0264-0.1723-0.02790.3523-0.0331-0.1317-0.00310.1981-0.0025-0.05380.2318-0.02510.29211.042830.585349.4613
62.5634-0.35211.0890.174-0.110.4610.1595-0.58910.18050.09250.08740.5865-0.1798-0.7144-0.02570.39390.00920.06790.59460.08940.521820.87376.265473.4412
72.3129-0.42870.13151.9837-0.28160.8145-0.0212-0.1717-0.61420.05560.02840.68080.1595-0.2098-0.03270.2549-0.0601-0.00440.25190.00980.4994-0.147610.234956.4356
82.8778-0.6787-0.79312.6380.00212.7683-0.0551-0.379-0.54470.19510.02440.43150.24740.00990.02340.2639-0.0441-0.0130.2790.0740.44984.14088.735860.3642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 27:143)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 144:188)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 189:226)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 227:353)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 361:531)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 532:560)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 561:627)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 628:688)

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