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- PDB-5upd: Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candid... -

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Basic information

Entry
Database: PDB / ID: 5upd
TitleMethyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)
ComponentsHistone-lysine N-methyltransferase NSD3
KeywordsTRANSFERASE / Structural Genomics Consortium / methyl transferase / SGC
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 / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTempel, W. / Yu, W. / Dong, A. / Cerovina, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)
Authors: Tempel, W. / Yu, W. / Dong, A. / Cerovina, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H.
History
DepositionFeb 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
SupersessionMar 8, 2017ID: 4YZ8
Revision 1.1Mar 8, 2017Group: Other
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,08922
Polymers26,4941
Non-polymers59521
Water2,594144
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.160, 62.810, 48.840
Angle α, β, γ (deg.)90.000, 109.780, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR-DETERMINED QUATERNARY STRUCTURE: not available

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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: 26494.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WHSC1L1, NSD3, DC28 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRARE-V2R
References: UniProt: Q9BZ95, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#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 / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.41 Å3/Da / Density % sol: 48.87 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.8→41.55 Å / Num. obs: 23067 / % possible obs: 98.9 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.064 / Rrim(I) all: 0.124 / Net I/σ(I): 11.1 / Num. measured all: 85056 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.853.20.714538316780.6260.4710.859296.2
8.06-41.553.40.0389122670.9970.0240.04531.894.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3OOI

3ooi


Resolution: 1.8→41.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.051 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ARP/WARP was used for automated model building. COOT was used for interactive model building. PHENIX.MOLPROBITY was used for validation of model geometry
RfactorNum. reflection% reflection
Rfree0.2182 1118 4.8 %
Rwork0.1839 --
obs0.1856 21949 98.79 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.29 Å2 / Biso mean: 24.398 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20.47 Å2
2---0.52 Å20 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 1.8→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 47 144 1835
Biso mean--19.74 29.57 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191781
X-RAY DIFFRACTIONr_bond_other_d0.0020.021600
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9792407
X-RAY DIFFRACTIONr_angle_other_deg1.0333.0063725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05523.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35615312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7171518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_mcbond_it2.2212.332864
X-RAY DIFFRACTIONr_mcbond_other2.2212.332864
X-RAY DIFFRACTIONr_mcangle_it3.4163.4871079
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 79 -
Rwork0.308 1596 -
all-1675 -
obs--95.93 %

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