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- PDB-10ax: Crystal structure of human SMYD1 in complex with Sinefungin -

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Basic information

Entry
Database: PDB / ID: 10ax
TitleCrystal structure of human SMYD1 in complex with Sinefungin
ComponentsHistone-lysine N-methyltransferase SMYD1
KeywordsTRANSFERASE / methytransferase / SMYD1 / SGC
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / histone H3K4 methyltransferase activity / Cardiogenesis / positive regulation of myotube differentiation / positive regulation of myoblast differentiation / heart development / transcription corepressor activity / negative regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
SMYD1, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain ...SMYD1, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain / SET domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
SINEFUNGIN / Histone-lysine N-methyltransferase SMYD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZeng, H. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of human SMYD1 in complex with Sinefungin
Authors: Zeng, H. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionJan 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SMYD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2636
Polymers55,6861
Non-polymers5785
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21390 Å2
Unit cell
Length a, b, c (Å)105.108, 105.108, 206.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Histone-lysine N-methyltransferase SMYD1 / SET and MYND domain-containing protein 1


Mass: 55685.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NB12, [histone H3]-lysine4 N-trimethyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 24 % (w/v) PEG 4000, 20 % (v/v) glycerol, 0.16 M magnesium chloride, 0.08 M Tris-HCl (pH 8.5)
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18049 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18049 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 16731 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.048 / Rrim(I) all: 0.163 / Χ2: 0.674 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.68-2.73110.9298090.8270.9510.2920.9750.59100
2.73-2.7810.50.768260.8670.9640.2450.7990.574100
2.78-2.8311.60.7278330.8690.9640.2220.760.578100
2.83-2.8911.60.6268020.9170.9780.1910.6550.612100
2.89-2.9511.60.5568210.9370.9840.170.5820.6100
2.95-3.0211.60.4818240.9490.9870.1470.5040.596100
3.02-3.0911.40.4238270.9630.990.130.4430.638100
3.09-3.1810.70.3728150.9650.9910.1180.390.622100
3.18-3.2711.30.2958340.9810.9950.0910.3080.627100
3.27-3.3811.80.2368220.9870.9970.0720.2470.649100
3.38-3.511.60.1958160.990.9980.060.2040.635100
3.5-3.6410.70.1638550.9920.9980.0520.1720.666100
3.64-3.811.60.1358140.9950.9990.0410.1410.652100
3.8-411.70.1088430.9970.9990.0330.1130.675100
4-4.2511.50.0898360.9980.9990.0270.0930.67399.9
4.25-4.5810.50.0718320.99810.0230.0740.67499.9
4.58-5.0411.50.0688610.99810.0210.0720.709100
5.04-5.7710.60.0768550.99810.0240.080.709100
5.77-7.2711.20.0748650.9970.9990.0230.0770.72100
7.27-509.90.0529410.9980.9990.0170.0551.282100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→46.89 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / SU B: 29.306 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.859 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28826 808 4.8 %RANDOM
Rwork0.21148 ---
obs0.21498 15897 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0 Å2
2---0.45 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.68→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 1 21 3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123637
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163321
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.8284916
X-RAY DIFFRACTIONr_angle_other_deg0.4081.7547599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.413520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34310582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2332.6951798
X-RAY DIFFRACTIONr_mcbond_other1.2322.6951798
X-RAY DIFFRACTIONr_mcangle_it2.1854.8422244
X-RAY DIFFRACTIONr_mcangle_other2.1844.8412245
X-RAY DIFFRACTIONr_scbond_it1.2282.7661839
X-RAY DIFFRACTIONr_scbond_other1.2282.7661839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1255.052673
X-RAY DIFFRACTIONr_long_range_B_refined3.70225.14039
X-RAY DIFFRACTIONr_long_range_B_other3.70125.114040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.748 Å
RfactorNum. reflection% reflection
Rfree0.461 48 -
Rwork0.304 1152 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: -48.3543 Å / Origin y: 18.0425 Å / Origin z: -26.0536 Å
111213212223313233
T0.0742 Å20.0056 Å2-0.009 Å2-0.0183 Å2-0.0055 Å2--0.0618 Å2
L2.9302 °20.3775 °20.1207 °2-0.7961 °20.2816 °2--0.3452 °2
S-0.015 Å °-0.1788 Å °0.2632 Å °-0.0689 Å °-0.0789 Å °0.0387 Å °0.0292 Å °-0.0019 Å °0.0939 Å °

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