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- PDB-4hc4: Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hc4 | ||||||
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Title | Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) | ||||||
![]() | Protein arginine N-methyltransferase 6 | ||||||
![]() | TRANSFERASE / HRMT1L6 / METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | ![]() histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-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 / protein modification process / base-excision repair / RMTs methylate histone arginines / cellular senescence / histone binding / methylation / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, A. / Zeng, H. / He, H. / El Bakkouri, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural basis of arginine asymmetrical dimethylation by PRMT6. Authors: Wu, H. / Zheng, W. / Eram, M.S. / Vhuiyan, M. / Dong, A. / Zeng, H. / He, H. / Brown, P. / Frankel, A. / Vedadi, M. / Luo, M. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.6 KB | Display | ![]() |
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PDB format | ![]() | 64.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qqkC ![]() 5hzmC ![]() 1g6qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
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Components
#1: Protein | Mass: 42074.559 Da / Num. of mol.: 1 / Mutation: A194V Source method: isolated from a genetically manipulated source Details: pFBOH-MHL / Source: (gene. exp.) ![]() ![]() References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Purified HRMT1L6 was complexed with SAH at 1:5 molar ratio of protein:SAH and crystallized by mixing 1 ul of the protein solution with 1 ul of the reservoir solution containing 15% PEG3350, ...Details: Purified HRMT1L6 was complexed with SAH at 1:5 molar ratio of protein:SAH and crystallized by mixing 1 ul of the protein solution with 1 ul of the reservoir solution containing 15% PEG3350, 0.1 M succinate acid, pH 7.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 33354 / Num. obs: 33354 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rsym value: 0.061 / Net I/σ(I): 42.1 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.746 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1G6Q Resolution: 1.97→33.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.378 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1408 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.407 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→33.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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