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- PDB-5hi7: Co-crystal structure of human SMYD3 with an aza-SAH compound -

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Basic information

Entry
Database: PDB / ID: 5hi7
TitleCo-crystal structure of human SMYD3 with an aza-SAH compound
ComponentsHistone-lysine N-methyltransferase SMYD3
KeywordsTRANSFERASE/INHIBITOR / SMYD3 / methyltransferase / oncology / inhibitor / TRANSFERASE-INHIBITOR complex
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 / nucleus / metal ion binding / 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. ...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
Chem-62X / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsElkins, P.A. / Bonnette, W.G.
CitationJournal: Structure / Year: 2016
Title: Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets.
Authors: Van Aller, G.S. / Graves, A.P. / Elkins, P.A. / Bonnette, W.G. / McDevitt, P.J. / Zappacosta, F. / Annan, R.S. / Dean, T.W. / Su, D.S. / Carpenter, C.L. / Mohammad, H.P. / Kruger, R.G.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SMYD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3188
Polymers49,5431
Non-polymers7757
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.470, 66.401, 104.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone-lysine N-methyltransferase SMYD3 / SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 49542.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Production host: unidentified baculovirus / Strain (production host): sf9
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-62X / 5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine


Mass: 452.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32N8O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: SMYD3 crystallization and soaking of GSK2807: SMYD3 (1-428) expressed in baculovirus and with SAH in the SAM-binding site was crystallized in sitting drops at 22C using 1uL fresh protein at ...Details: SMYD3 crystallization and soaking of GSK2807: SMYD3 (1-428) expressed in baculovirus and with SAH in the SAM-binding site was crystallized in sitting drops at 22C using 1uL fresh protein at 8.9mg/mL with the addition of 1uL mother liquor (200mM MgOAc Tetrahydrate, 20% PEG 3350). Crystals grew to a large size but varied in quantity when set up in replicates. A seed stock was formed from these crystals and added at 20% to the mother liquor solution prior to plate setup. Crystals of large size were then created with 1.3uL protein and 1.3uL of mother liquor containing seeds in a sitting drop MRC-2 plate (Hampton Research). Crystal nucleation occurred overnight and reached maximum size in 4 days

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46288 / % possible obs: 99.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 26.4 Å2 / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIXdev_1801refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→44.709 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1211 5.17 %random selection
Rwork0.1984 ---
obs0.1999 23433 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 39 119 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033395
X-RAY DIFFRACTIONf_angle_d0.6264612
X-RAY DIFFRACTIONf_dihedral_angle_d11.8971246
X-RAY DIFFRACTIONf_chiral_restr0.037521
X-RAY DIFFRACTIONf_plane_restr0.004592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.23610.27171350.23032454X-RAY DIFFRACTION100
2.2361-2.33790.28361240.22262461X-RAY DIFFRACTION100
2.3379-2.46120.27541180.22692458X-RAY DIFFRACTION100
2.4612-2.61530.23571430.21842448X-RAY DIFFRACTION100
2.6153-2.81720.28411500.21472460X-RAY DIFFRACTION100
2.8172-3.10070.23121400.20682467X-RAY DIFFRACTION100
3.1007-3.54920.20151410.19072464X-RAY DIFFRACTION99
3.5492-4.4710.19571300.16632468X-RAY DIFFRACTION98
4.471-44.71850.20271300.19542542X-RAY DIFFRACTION96
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)
10.94120.54470.97121.04270.46256.20030.0258-0.10290.09420.2667-0.01530.0821-0.05720.1333-0.0250.1978-0.00320.04090.2701-0.03040.28048.7044-3.4687-5.0462
22.9711-0.9539-0.53012.4863-0.07273.2539-0.0363-0.2268-0.12250.21310.0007-0.0020.18690.04770.05160.1937-0.0384-0.00350.1521-0.00990.189913.5955-17.7629-5.2762
30.73970.4704-0.04741.3545-0.25440.24340.00230.01160.04160.0640.003-0.0522-0.00690.0089-0.00260.2282-0.00210.02110.186-0.00750.195521.77087.5702-18.5853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:93)
2X-RAY DIFFRACTION2chain 'A' and (resseq 94:186)
3X-RAY DIFFRACTION3chain 'A' and (resseq 187:427)

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