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- PDB-4h12: The crystal structure of methyltransferase domain of human SET do... -

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Basic information

Entry
Database: PDB / ID: 4h12
TitleThe crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine
ComponentsHistone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / methyltransferase / SET domain-containing protein 2 / S-adenosyl-L-homocysteine / structural genomics / Structural Genomics Consortium / SGC / activator / chromatin regulator / DNA-binding / methylation / nucleus / phosphoprotein / transcription / transcription regulation
Function / homology
Function and homology information


mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus / pericardium development / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / alpha-tubulin binding / positive regulation of interferon-alpha production / mismatch repair / positive regulation of autophagy / forebrain development / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / response to organic cyclic compound / PKMTs methylate histone lysines / chromosome / regulation of gene expression / angiogenesis / defense response to virus / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Beta-clip-like ...Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Beta-clip-like / SET domain / TFIIS/LEDGF domain superfamily / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain superfamily / WW domain / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsAmaya, M.F. / Dong, A. / Zeng, H. / Mackenzie, F. / Bunnage, M. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Amaya, M.F. / Dong, A. / Zeng, H. / Mackenzie, F. / Bunnage, M. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2.
Authors: Zheng, W. / Ibanez, G. / Wu, H. / Blum, G. / Zeng, H. / Dong, A. / Li, F. / Hajian, T. / Allali-Hassani, A. / Amaya, M.F. / Siarheyeva, A. / Yu, W. / Brown, P.J. / Schapira, M. / Vedadi, M. / Min, J. / Luo, M.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 3, 2012ID: 3H6L
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5726
Polymers31,9551
Non-polymers6165
Water2,234124
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.293, 76.663, 78.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase SETD2 / HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin- ...HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin-interacting protein B / Lysine N-methyltransferase 3A / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 31955.488 Da / Num. of mol.: 1 / Fragment: methyltransferase domain (UNP residues 1434-1711)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 / Plasmid: pET28-Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q9BYW2, 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein (1:10 molar ratio of SETD2:AdoMet) + 1 uL reservoir solution (30% PEG2000 MME, 0.1 M potassium thiocyanate), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.991→50 Å / Num. obs: 21811 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.991-2.032.90.753190.7
2.03-2.073.40.72196.2
2.07-2.1140.665197.5
2.11-2.1550.53198.8
2.15-2.26.50.436199.4
2.2-2.257.20.414199.4
2.25-2.317.40.37199.3
2.31-2.377.70.302199.9
2.37-2.447.80.2651100
2.44-2.527.90.2281100
2.52-2.618.10.2061100
2.61-2.7180.1731100
2.71-2.8480.1271100
2.84-2.9980.1081100
2.99-3.1780.0941100
3.17-3.427.90.0761100
3.42-3.767.80.07199.8
3.76-4.317.60.074199.6
4.31-5.437.40.072199.4
5.43-5070.064198

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R3A

2r3a


Resolution: 2.06→38.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.679 / SU ML: 0.126 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24904 1011 5.1 %RANDOM
Rwork0.20741 ---
obs0.20953 18905 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.608 Å2
Baniso -1Baniso -2Baniso -3
1-5.62 Å20 Å20 Å2
2---4.55 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.06→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 30 124 1932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021853
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9542506
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31824.02387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74915288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.051511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211434
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 71 -
Rwork0.332 1342 -
obs--97.72 %
Refinement TLS params.Method: refined / Origin x: 1.8258 Å / Origin y: 16.0767 Å / Origin z: 14.4687 Å
111213212223313233
T0.0179 Å2-0.0196 Å2-0.0034 Å2-0.0471 Å20.0068 Å2--0.0178 Å2
L1.362 °2-1.2652 °2-0.4221 °2-3.082 °20.4505 °2--0.9939 °2
S-0.0397 Å °-0.0916 Å °-0.0266 Å °0.1361 Å °0.0065 Å °0.0011 Å °0.0736 Å °-0.0018 Å °0.0332 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1447 - 1691
2X-RAY DIFFRACTION1A1801 - 1805
3X-RAY DIFFRACTION1A1901 - 2024

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