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- PDB-6cen: Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21 -

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Basic information

Entry
Database: PDB / ID: 6cen
TitleCrystal Structure of WHSC1L1 in Complex with Inhibitor PEP21
Components
  • ACE-GLY-VAL-NLE-ARG-ILE-NH2
  • Histone-lysine N-methyltransferase NSD3
KeywordsTRANSFERASE/INHIBITOR / Histone-lysine N-methyltransferase NSD3 / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain ...: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.61 Å
AuthorsBoriack-Sjodin, P.A. / Swinger, K. / Farrow, N.A.
CitationJournal: PLoS ONE / Year: 2018
Title: Identification of a peptide inhibitor for the histone methyltransferase WHSC1.
Authors: Morrison, M.J. / Boriack-Sjodin, P.A. / Swinger, K.K. / Wigle, T.J. / Sadalge, D. / Kuntz, K.W. / Scott, M.P. / Janzen, W.P. / Chesworth, R. / Duncan, K.W. / Harvey, D.M. / Lampe, J.W. / ...Authors: Morrison, M.J. / Boriack-Sjodin, P.A. / Swinger, K.K. / Wigle, T.J. / Sadalge, D. / Kuntz, K.W. / Scott, M.P. / Janzen, W.P. / Chesworth, R. / Duncan, K.W. / Harvey, D.M. / Lampe, J.W. / Mitchell, L.H. / Copeland, R.A.
History
DepositionFeb 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD3
D: ACE-GLY-VAL-NLE-ARG-ILE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1126
Polymers26,5172
Non-polymers5954
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-10 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.870, 62.660, 48.600
Angle α, β, γ (deg.)90.000, 107.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase NSD3 / Nuclear SET domain-containing protein 3 / Protein whistle / WHSC1-like 1 isoform 9 with ...Nuclear SET domain-containing protein 3 / Protein whistle / WHSC1-like 1 isoform 9 with methyltransferase activity to lysine / Wolf-Hirschhorn syndrome candidate 1-like protein 1 / WHSC1-like protein 1


Mass: 25935.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD3, WHSC1L1, DC28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BZ95, histone-lysine N-methyltransferase
#2: Protein/peptide ACE-GLY-VAL-NLE-ARG-ILE-NH2


Mass: 581.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 20% w/v PEG5000MME

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→46.29 Å / Num. obs: 29790 / % possible obs: 93.8 % / Redundancy: 3.72 % / Net I/σ(I): 20.48
Reflection shellResolution: 1.61→1.69 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 1.61→46.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.109 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1491 5 %RANDOM
Rwork0.1789 ---
obs0.1807 28299 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.59 Å2 / Biso mean: 25.933 Å2 / Biso min: 9.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20.09 Å2
2--0.16 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.61→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 31 226 2092
Biso mean--13.75 32.09 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191948
X-RAY DIFFRACTIONr_bond_other_d0.020.021857
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9912627
X-RAY DIFFRACTIONr_angle_other_deg1.7663.0054274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3824.10595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62315351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7981517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212205
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02450
LS refinement shellResolution: 1.61→1.652 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 100 -
Rwork0.283 1820 -
all-1920 -
obs--81.56 %

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