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- PDB-3mek: Crystal Structure of Human Histone-Lysine N-methyltransferase SMY... -

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Basic information

Entry
Database: PDB / ID: 3mek
TitleCrystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine
ComponentsSET and MYND domain-containing protein 3
KeywordsTRANSFERASE / histone methyltransferase / SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1 / histone H3 / di-methylation / tri-methylation / transcriptional activation / DNA-binding / MYND-type zinc finger / SET domain / chromatin modification / Alternative splicing / Chromatin regulator / Cytoplasm / Metal-binding / Methyltransferase / Nucleus / S-adenosyl-L-methionine / Zinc / Zinc-finger / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. ...Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Annexin V; domain 1 / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLam, R. / Dombrovski, L. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine
Authors: Lam, R. / Dombrovski, L. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Wu, H.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SET and MYND domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5805
Polymers49,9851
Non-polymers5954
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.809, 65.923, 108.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 49985.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THEY BASED THE TEMPLATE FOR SMYD3 ON THE MGC CLONE (ACCESSION BC031010, VERSION ...AUTHORS STATE THAT THEY BASED THE TEMPLATE FOR SMYD3 ON THE MGC CLONE (ACCESSION BC031010, VERSION BC031010.1, GI:21410973)

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / pH: 8
Details: 20% PEG3350, 0.2M Mg Formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010
Details: ROSENBAUM-ROCK HIGH- RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26234 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.423 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.09 Å / D res low: 44.7 Å / FOM acentric: 0.336 / FOM centric: 0.135 / Reflection acentric: 23070 / Reflection centric: 3102
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.0944.7230703102
ANO_10.81602.0944.7230640
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_19.18-44.700218146
ISO_16.56-9.1800437153
ISO_15.37-6.5600578158
ISO_14.66-5.3700696152
ISO_14.17-4.6600809152
ISO_13.81-4.1700893158
ISO_13.53-3.8100973156
ISO_13.31-3.53001062155
ISO_13.12-3.31001121159
ISO_12.96-3.12001203155
ISO_12.82-2.96001266156
ISO_12.7-2.82001316159
ISO_12.6-2.7001403153
ISO_12.5-2.6001430159
ISO_12.42-2.5001486160
ISO_12.34-2.42001536145
ISO_12.27-2.34001616162
ISO_12.21-2.27001657153
ISO_12.15-2.21001709162
ISO_12.09-2.15001661149
ANO_19.18-44.70.44802180
ANO_16.56-9.180.39204370
ANO_15.37-6.560.42405780
ANO_14.66-5.370.56406950
ANO_14.17-4.660.65608090
ANO_13.81-4.170.69408920
ANO_13.53-3.810.69709720
ANO_13.31-3.530.681010620
ANO_13.12-3.310.742011210
ANO_12.96-3.120.71012030
ANO_12.82-2.960.782012660
ANO_12.7-2.820.786013160
ANO_12.6-2.70.832014030
ANO_12.5-2.60.878014300
ANO_12.42-2.50.912014860
ANO_12.34-2.420.931015360
ANO_12.27-2.340.953016160
ANO_12.21-2.270.965016540
ANO_12.15-2.210.976017090
ANO_12.09-2.150.984016610
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-13.473-14.43-16.907SE21.991.86
2-20.36-1.728-24.746SE24.571.48
3-26.087-15.522-14.923SE23.951.45
4-14.56-16.6-13.883SE28.681.58
5-29.198-1.78-27.643SE27.341.29
6-39.273-4.852-7.813SE41.821.6
7-56.0166.5860.434SE32.621.14
8-26.0613.328-21.465SE30.571.16
9-23.109-17.894-21.765SE27.311.13
10-16.98-6.655-14.42SE52.151.49
11-34.763-53.985-1.295SE32.241
12-44.591-39.18-11.785SE18.30.67
13-39.774-26.521-23.767SE25.820.74
14-41.404-27.181-3.562SE34.170.8
15-44.664-49.659-4.14SE42.520.85
16-26.099-28.716-16.638SE53.361.04
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
9.18-44.70.630.211218146
6.56-9.180.6450.202437153
5.37-6.560.6140.211578158
4.66-5.370.5410.144696152
4.17-4.660.4590.12809152
3.81-4.170.4390.142893158
3.53-3.810.4480.11973156
3.31-3.530.4380.1291062155
3.12-3.310.4010.1151121159
2.96-3.120.4170.1311203155
2.82-2.960.3850.1331266156
2.7-2.820.3830.141316159
2.6-2.70.3450.1231403153
2.5-2.60.3040.1321430159
2.42-2.50.2740.1141486160
2.34-2.420.2550.1141536145
2.27-2.340.2230.1051616162
2.21-2.270.2030.1191657153
2.15-2.210.1810.1131709162
2.09-2.150.1690.1041661149
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 26172
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.15-10066.70.705510
6.4-8.1568.50.852510
5.55-6.457.60.852508
4.99-5.5564.20.886558
4.57-4.9961.10.896620
4.24-4.5766.40.916648
3.97-4.2461.40.925698
3.75-3.9761.90.921737
3.56-3.7562.30.903772
3.4-3.5663.40.901822
3.25-3.461.50.892849
3.13-3.2567.50.884869
3.01-3.1364.90.87909
2.91-3.0163.90.849948
2.82-2.9166.10.853980
2.74-2.82670.8521014
2.66-2.7466.10.8441012
2.59-2.6667.50.8331066
2.53-2.5969.90.8431092
2.47-2.5369.60.8491104
2.41-2.4773.80.8291148
2.36-2.4174.90.8361150
2.31-2.3674.60.8241189
2.26-2.3174.50.8181201
2.22-2.2676.40.811254
2.18-2.2278.70.7841240
2.14-2.1879.60.7831265
2.09-2.1478.80.7141499

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6.1phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1328 5.074 %RANDOM
Rwork0.174 ---
obs0.17584 26172 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 18.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.027 Å20 Å20 Å2
2--0.028 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 30 175 3544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9844666
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0424.013157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55915626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212585
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21567
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22402
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6281.52129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26123428
X-RAY DIFFRACTIONr_scbond_it2.32131322
X-RAY DIFFRACTIONr_scangle_it3.8534.51234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 94 -
Rwork0.187 1716 -
obs--96.02 %
Refinement TLS params.Method: refined / Origin x: 12.208 Å / Origin y: 32.592 Å / Origin z: 12.902 Å
111213212223313233
T0.0082 Å2-0.0053 Å2-0.0015 Å2-0.0092 Å20.0014 Å2--0.0184 Å2
L0.1889 °2-0.1144 °2-0.1562 °2-0.3384 °20.1611 °2--0.4733 °2
S0.0155 Å °0.0002 Å °0.0098 Å °-0.0274 Å °-0.0026 Å °-0.0124 Å °-0.0542 Å °0.0211 Å °-0.0129 Å °

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