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- PDB-4jlg: SETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine -

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Basic information

Entry
Database: PDB / ID: 4jlg
TitleSETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine
ComponentsHistone-lysine N-methyltransferase SETD7
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Methyltransferase / SET domain / histone modification / transcription regulation / histone lysine methyltransferase / inhibitor / S-adenosyl-L-methionine / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding / chromatin organization / chromosome / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-1L8 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsDong, A. / Wu, H. / Zeng, H. / El Bakkouri, M. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. ...Dong, A. / Wu, H. / Zeng, H. / El Bakkouri, M. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: (R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells.
Authors: Barsyte-Lovejoy, D. / Li, F. / Oudhoff, M.J. / Tatlock, J.H. / Dong, A. / Zeng, H. / Wu, H. / Freeman, S.A. / Schapira, M. / Senisterra, G.A. / Kuznetsova, E. / Marcellus, R. / Allali- ...Authors: Barsyte-Lovejoy, D. / Li, F. / Oudhoff, M.J. / Tatlock, J.H. / Dong, A. / Zeng, H. / Wu, H. / Freeman, S.A. / Schapira, M. / Senisterra, G.A. / Kuznetsova, E. / Marcellus, R. / Allali-Hassani, A. / Kennedy, S. / Lambert, J.P. / Couzens, A.L. / Aman, A. / Gingras, A.C. / Al-Awar, R. / Fish, P.V. / Gerstenberger, B.S. / Roberts, L. / Benn, C.L. / Grimley, R.L. / Braam, M.J. / Rossi, F.M. / Sudol, M. / Brown, P.J. / Bunnage, M.E. / Owen, D.R. / Zaph, C. / Vedadi, M. / Arrowsmith, C.H.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Structure summary
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 SETD7
B: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,16431
Polymers59,3682
Non-polymers1,79629
Water7,098394
1
A: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58220
Polymers29,6841
Non-polymers89819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58211
Polymers29,6841
Non-polymers89810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.742, 57.984, 64.932
Angle α, β, γ (deg.)83.330, 71.420, 70.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Histone-lysine N-methyltransferase SETD7 / Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET ...Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET domain-containing protein 7 / SET7/9


Mass: 29683.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-1L8 / 8-fluoro-N-{(2R)-1-oxo-1-(pyrrolidin-1-yl)-3-[3-(trifluoromethyl)phenyl]propan-2-yl}-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide


Mass: 499.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25F4N3O3S
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 25 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG 3500, 0.2 M Lithium Sulfate, 0.1 M BisTris pH 6.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.896→50 Å / Num. all: 45882 / Num. obs: 45882 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.596 / Net I/σ(I): 38.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.896-1.934.80.22419390.858180.6
1.93-1.974.90.22219970.798183.7
1.97-2.014.90.19921110.912187.8
2.01-2.055.10.16522250.99192
2.05-2.095.20.15222750.981194.4
2.09-2.145.40.14823051.044195.7
2.14-2.195.60.14523341.046197.1
2.19-2.255.70.13623271.105197
2.25-2.325.80.12423701.204197.1
2.32-2.395.90.11623321.189197.5
2.39-2.485.90.10623551.27197.8
2.48-2.5860.09523391.434197.4
2.58-2.760.08723461.569198.1
2.7-2.8460.07723711.719198.2
2.84-3.025.90.06723482.051198.4
3.02-3.255.90.05923942.353198.5
3.25-3.585.80.05123892.555198.6
3.58-4.095.80.04623702.636198.9
4.09-5.165.90.04123872.431199.2
5.16-505.70.04323682.714198.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9S

1o9s


Resolution: 1.896→30.75 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2395 / WRfactor Rwork: 0.2183 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8119 / SU B: 3.751 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1653 / SU Rfree: 0.1445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1454 3.2 %RANDOM
Rwork0.2113 ---
all0.2121 45882 --
obs0.2121 45881 94.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.49 Å2 / Biso mean: 30.5528 Å2 / Biso min: 2.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.59 Å2-1.54 Å2
2--0.16 Å2-2.99 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.896→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 147 394 4313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224072
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9925581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74524.211171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.2631515
X-RAY DIFFRACTIONr_chiral_restr0.070.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213157
X-RAY DIFFRACTIONr_mcbond_it0.5671.52515
X-RAY DIFFRACTIONr_mcangle_it1.06324072
X-RAY DIFFRACTIONr_scbond_it1.47631557
X-RAY DIFFRACTIONr_scangle_it2.4044.51500
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 92 -
Rwork0.286 2531 -
all-2623 -
obs--72.72 %

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