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- PDB-4qpp: The Crystal Structure of Human HMT1 hnRNP methyltransferase-like ... -

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Basic information

Entry
Database: PDB / ID: 4qpp
TitleThe Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with compound DS-421 (2-{4-[3-CHLORO-2-(2-METHOXYPHENYL)-1H-INDOL-5-YL]PIPERIDIN-1-YL}-N-METHYLETHANAMINE
Components
  • POLY-UNK
  • Protein arginine N-methyltransferase 6
KeywordsTransferase/transferase inhibitor / HRMT1L6 / methyltransferase-like protein / Structural Genomics / Structural Genomics Consortium / SGC / transferase / DS421 / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H3R2 methyltransferase activity / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / : / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H3R2 methyltransferase activity / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / : / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / base-excision repair / protein modification process / RMTs methylate histone arginines / cellular senescence / histone binding / methylation / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / 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 / Distorted Sandwich ...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 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-36S / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDong, A. / Zeng, H. / Smil, D. / Walker, J.R. / He, H. / Eram, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. ...Dong, A. / Zeng, H. / Smil, D. / Walker, J.R. / He, H. / Eram, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with compound DS-421
Authors: Zeng, H. / Dong, A. / Smil, D. / Walker, J.R. / He, H. / Eram, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Brown, P.J. / Wu, H.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
B: Protein arginine N-methyltransferase 6
C: Protein arginine N-methyltransferase 6
D: POLY-UNK
E: POLY-UNK
F: POLY-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,41212
Polymers128,0656
Non-polymers2,3476
Water5,080282
1
A: Protein arginine N-methyltransferase 6
D: POLY-UNK
hetero molecules

A: Protein arginine N-methyltransferase 6
D: POLY-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9418
Polymers85,3774
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Buried area4010 Å2
ΔGint-38 kcal/mol
Surface area27200 Å2
2
B: Protein arginine N-methyltransferase 6
E: POLY-UNK
hetero molecules

B: Protein arginine N-methyltransferase 6
E: POLY-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9418
Polymers85,3774
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Buried area3940 Å2
ΔGint-36 kcal/mol
Surface area26960 Å2
3
C: Protein arginine N-methyltransferase 6
F: POLY-UNK
hetero molecules

C: Protein arginine N-methyltransferase 6
F: POLY-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9418
Polymers85,3774
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area3940 Å2
ΔGint-37 kcal/mol
Surface area27140 Å2
Unit cell
Length a, b, c (Å)133.884, 133.884, 133.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Protein arginine N-methyltransferase 6 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N- ...Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 42074.559 Da / Num. of mol.: 3 / Mutation: A194V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRMT1L6, PRMT6 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Protein/peptide POLY-UNK


Mass: 613.749 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-36S / 2-{4-[3-chloro-2-(2-methoxyphenyl)-1H-indol-5-yl]piperidin-1-yl}-N-methylethanamine


Mass: 397.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H28ClN3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M NaForm, 0.1 M NaoAc, pH 4.6, vapor diffusion hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 336892 / Num. obs: 41807 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.133 / Χ2: 1.049 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.52-2.568.20.90420510.7861100
2.56-2.618.20.8220420.7711100
2.61-2.668.20.79320550.781100
2.66-2.718.20.66820600.821100
2.71-2.778.20.54220390.8291100
2.77-2.848.20.48520590.8331100
2.84-2.918.20.41620900.8521100
2.91-2.998.20.31420480.8931100
2.99-3.088.20.2820540.9341100
3.08-3.178.20.22820750.961100
3.17-3.298.20.17420651.0031100
3.29-3.428.20.14820861.0341100
3.42-3.588.10.1220851.0751100
3.58-3.768.10.09620701.1511100
3.76-48.10.0920981.2431100
4-4.3180.08221201.4551100
4.31-4.747.90.08221131.9361100
4.74-5.437.80.07321281.6811100
5.43-6.837.60.06121681.0621100
6.83-507.30.03223010.8971100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4HC4

4hc4


Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.379 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.496 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 830 2 %RANDOM
Rwork0.1907 ---
obs0.1915 41519 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.1 Å2 / Biso mean: 37.597 Å2 / Biso min: 2.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7685 0 155 282 8122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198130
X-RAY DIFFRACTIONr_bond_other_d0.0020.027589
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.97611051
X-RAY DIFFRACTIONr_angle_other_deg0.8933.00417424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2851021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87623.559354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.154151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8051558
X-RAY DIFFRACTIONr_chiral_restr0.0610.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021891
X-RAY DIFFRACTIONr_mcbond_it1.2953.7344057
X-RAY DIFFRACTIONr_mcbond_other1.2943.7334056
X-RAY DIFFRACTIONr_mcangle_it2.2485.5885072
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 63 -
Rwork0.252 2911 -
all-2974 -
obs--99.97 %

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