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- PDB-4fmu: Crystal structure of Methyltransferase domain of human SET domain... -

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Basic information

Entry
Database: PDB / ID: 4fmu
TitleCrystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF
ComponentsHistone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / Methyltransferase / SET domain-containing protein 2 / Pr-SNF
Function / homology
Function and homology information


peptidyl-lysine trimethylation / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / histone H3K36 methyltransferase activity / response to alkaloid / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity ...peptidyl-lysine trimethylation / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / histone H3K36 methyltransferase activity / response to alkaloid / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity / positive regulation of ossification / 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 / positive regulation of interferon-alpha production / alpha-tubulin binding / mismatch repair / positive regulation of autophagy / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / stem cell differentiation / transcription elongation by RNA polymerase II / PKMTs methylate histone lysines / chromosome / regulation of gene expression / defense response to virus / regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) 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 superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / TFIIS/LEDGF domain superfamily / WW domain / WW/rsp5/WWP domain signature. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / SET domain / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain superfamily / SET domain profile. / SET domain / WW domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-0UM / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDong, A. / Zeng, H. / Ibanez, G. / Zheng, W. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. ...Dong, A. / Zeng, H. / Ibanez, G. / Zheng, W. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Luo, M. / 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
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 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 / software / 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 / _software.name / _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)32,57518
Polymers31,9551
Non-polymers62017
Water1,67593
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.547, 77.277, 78.864
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)V2RpRARE
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-0UM / (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid


Mass: 423.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N7O5
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 10% isoprpanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03321 Å
DetectorType: MAR 300 CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19073 / Num. obs: 18501 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 38.63 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 42.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.08 / Num. unique all: 769 / Rsym value: 0.221 / % possible all: 82.3

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
MOLREPphasing
BUSTER2.10.0refinement
Coot0.6model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H6L

3h6l
PDB Unreleased entry


Resolution: 2.1→35.12 Å / Cor.coef. Fo:Fc: 0.9135 / Cor.coef. Fo:Fc free: 0.8853 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 937 5.08 %RANDOM
Rwork0.1935 ---
all0.1954 18501 --
obs0.1954 18431 97.04 %-
Displacement parametersBiso mean: 46.23 Å2
Baniso -1Baniso -2Baniso -3
1--23.9807 Å20 Å20 Å2
2--13.5201 Å20 Å2
3---10.4607 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 46 93 1932
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011888HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d646SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes282HARMONIC5
X-RAY DIFFRACTIONt_it1888HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion16.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion242SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2154SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2405 147 5.61 %
Rwork0.2127 2471 -
all0.2141 2618 -
obs--97.04 %

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