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- PDB-6mon: Crystal structure of human SMYD2 in complex with Nle-peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 6mon
TitleCrystal structure of human SMYD2 in complex with Nle-peptide inhibitor
Components
  • LYS-LEU-NLE-SER-LYS-ARG-GLY
  • N-lysine methyltransferase SMYD2
KeywordsTRANSFERASE / methyltransferase / norleucine / complex
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.711 Å
AuthorsSpellmon, N. / Cornett, E. / Brunzelle, J. / Rothbart, S. / Yang, Z.
CitationJournal: Sci Adv / Year: 2018
Title: A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity.
Authors: Cornett, E.M. / Dickson, B.M. / Krajewski, K. / Spellmon, N. / Umstead, A. / Vaughan, R.M. / Shaw, K.M. / Versluis, P.P. / Cowles, M.W. / Brunzelle, J. / Yang, Z. / Vega, I.E. / Sun, Z.W. / Rothbart, S.B.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
B: N-lysine methyltransferase SMYD2
C: LYS-LEU-NLE-SER-LYS-ARG-GLY
D: LYS-LEU-NLE-SER-LYS-ARG-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,54913
Polymers100,2954
Non-polymers1,2539
Water1267
1
A: N-lysine methyltransferase SMYD2
C: LYS-LEU-NLE-SER-LYS-ARG-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8207
Polymers50,1482
Non-polymers6735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-7 kcal/mol
Surface area20520 Å2
MethodPISA
2
B: N-lysine methyltransferase SMYD2
D: LYS-LEU-NLE-SER-LYS-ARG-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7286
Polymers50,1482
Non-polymers5814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.728, 153.728, 53.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 5 - 433 / Label seq-ID: 1 - 429

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein N-lysine methyltransferase SMYD2 / HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain- ...HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain-containing protein 2


Mass: 49343.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide LYS-LEU-NLE-SER-LYS-ARG-GLY


Mass: 804.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 16 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20.5% PEG 3350, 5.9% ethanol, 0.1M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.71→153.73 Å / Num. obs: 34429 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.055 / Net I/σ(I): 11.9
Reflection shellResolution: 2.71→2.86 Å / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4982 / CC1/2: 0.519 / Rpim(I) all: 0.795 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimless0.5.32data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KJK

5kjk


Resolution: 2.711→51.243 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.3
RfactorNum. reflection% reflection
Rfree0.2267 1601 4.65 %
Rwork0.2105 --
obs0.2112 34396 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.5 Å2 / Biso mean: 75.7222 Å2 / Biso min: 35.81 Å2
Refinement stepCycle: final / Resolution: 2.711→51.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7003 0 64 7 7074
Biso mean--62.86 56.94 -
Num. residues----870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067244
X-RAY DIFFRACTIONf_angle_d1.0569725
X-RAY DIFFRACTIONf_chiral_restr0.0451035
X-RAY DIFFRACTIONf_plane_restr0.0061248
X-RAY DIFFRACTIONf_dihedral_angle_d16.0952758
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4304X-RAY DIFFRACTION0.558TORSIONAL
12B4304X-RAY DIFFRACTION0.558TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7111-2.79860.34811330.324729813114100
2.7986-2.89860.32131710.301629013072100
2.8986-3.01470.29751180.285329923110100
3.0147-3.15190.29441460.270629673113100
3.1519-3.3180.31221310.266329773108100
3.318-3.52580.27571150.237829733088100
3.5258-3.7980.24481220.220430113133100
3.798-4.180.23951800.198729563136100
4.18-4.78450.17321710.170429653136100
4.7845-6.02650.19541590.184830023161100
6.0265-51.25180.18761550.1733070322599
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)
11.7870.01620.73220.7752-0.2751.7087-0.2105-0.04420.15470.1648-0.06830.19370.007-0.2208-0.01460.44690.1231-0.04780.2818-0.04290.4736160.627436.6044-34.9646
20.45860.03890.05080.20480.4671.0514-0.255-0.00120.11310.06570.0453-0.0209-0.21760.4592-0.00010.54130.0123-0.09330.43860.11420.5291183.5995441.0895-32.6549
30.2715-0.07310.19760.6890.18381.141-0.34230.2999-0.2265-0.32630.008-0.2333-0.21721.527-0.05190.43280.07450.03030.97960.21930.5214190.1495433.3076-47.226
40.22530.0750.13850.44140.58690.81050.24450.1534-0.24070.0125-0.385-0.07010.87610.0416-0.00110.82070.38140.11950.58960.05890.6865183.1133415.9733-37.1261
51.7559-0.0492-0.59790.8328-0.02592.7431-0.2456-0.03050.02980.1483-0.0372-0.1547-0.07670.1432-0.00440.3810.0777-0.02810.2086-0.00240.3946223.9984409.8576-62.0576
61.0828-0.02230.00891.9953-0.40161.071-0.17440.1991-0.1739-0.0605-0.00180.00880.0201-0.897-0.55240.3570.04930.01760.6995-0.21260.3199198.2864406.5906-66.4398
70.8577-0.38380.39640.3081-0.28492.0299-0.61470.23620.53520.2879-0.3763-0.036-1.6238-1.2059-1.67020.62990.8977-0.24120.6511-0.23910.5265200.9247426.5383-68.0112
80.6648-0.3323-0.15120.16650.070.1040.02040.303-0.2018-0.2505-0.2916-0.30190.32580.3095-0.0180.9075-0.1868-0.00930.78820.13540.8565176.1692437.2696-35.9839
90.3316-0.4424-1.00541.14252.11124.1274-0.1940.18590.617-0.282-0.23220.402-0.6114-0.29240.09410.8552-0.25380.11550.9904-0.20851.0616210.9291409.1537-64.5535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 182 )A5 - 182
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 310 )A183 - 310
3X-RAY DIFFRACTION3chain 'A' and (resid 311 through 397 )A311 - 397
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 433 )A398 - 433
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 212 )B5 - 212
6X-RAY DIFFRACTION6chain 'B' and (resid 213 through 355 )B213 - 355
7X-RAY DIFFRACTION7chain 'B' and (resid 356 through 433 )B356 - 433
8X-RAY DIFFRACTION8chain 'C' and (resid -1 through 3 )C369 - 373
9X-RAY DIFFRACTION9chain 'D' and (resid -2 through 4 )D368 - 374

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