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- PDB-5vc8: Crystal structure of the WHSC1 PWWP1 domain -

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Basic information

Entry
Database: PDB / ID: 5vc8
TitleCrystal structure of the WHSC1 PWWP1 domain
Components
  • DNA (5'-D(P*CP*TP*(DN))-3')
  • Histone-lysine N-methyltransferase NSD2
  • dodeca-2-deoxy-nucleotide, poorly resolved by electron density
KeywordsDNA BINDING PROTEIN / PWWP domain / Structural Genomics Consortium
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / bone development / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / methylation / sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich 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. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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 / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsQin, S. / Tempel, W. / Dong, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.
Authors: Zhang, M. / Yang, Y. / Zhou, M. / Dong, A. / Yan, X. / Loppnau, P. / Min, J. / Liu, Y.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD2
B: Histone-lysine N-methyltransferase NSD2
W: dodeca-2-deoxy-nucleotide, poorly resolved by electron density
X: dodeca-2-deoxy-nucleotide, poorly resolved by electron density
Y: dodeca-2-deoxy-nucleotide, poorly resolved by electron density
Z: DNA (5'-D(P*CP*TP*(DN))-3')


Theoretical massNumber of molelcules
Total (without water)44,13045
Polymers44,1306
Non-polymers039
Water1,910106
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-28 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.990, 82.990, 115.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsunreliable DNA coordinates does not allow for higher-level biological assembly prediction.

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Components

#1: Protein Histone-lysine N-methyltransferase NSD2 / Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / ...Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / Protein trithorax-5 / Wolf-Hirschhorn syndrome candidate 1 protein


Mass: 16207.175 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: O96028, histone-lysine N-methyltransferase
#2: DNA chain dodeca-2-deoxy-nucleotide, poorly resolved by electron density


Mass: 3662.404 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*(DN))-3')


Mass: 728.513 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Interpretation of weak electron density in terms of an unidentified fragment of the dodecadeoxynucleotide.
Source: (synth.) synthetic construct (others)
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 39 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.27 Å3/Da / Density % sol: 45.71 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1M sodium iodide,0.1M magnesium nitrate, 25%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→37.11 Å / Num. obs: 38039 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 28.5 / Num. measured all: 543668 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8514.31.060.8030.2891.099100
8.05-37.11110.0580.9970.0180.06199.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→37.11 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.51
Details: The nucleic acid component of this model is based on weak and discontinuous density. It has been included as an interpretative guide to some features in the difference maps, but must be ...Details: The nucleic acid component of this model is based on weak and discontinuous density. It has been included as an interpretative guide to some features in the difference maps, but must be considered unreliable. Moreover, the current definition of the asymmetric unit does not aim to reflect a biologically relevant protein:DNA interface. The poor fit of the side chains of WHSC1 residues Glu-278 to electron density maps suggests that these residues have been mutated relative to the provided amino acid sequence. The structure was solved by single wavelength anomalous diffraction using an isomorphous crystal and data collected at APS beam line 23-IDB.
RfactorNum. reflection% reflection
Rfree0.2286 2661 3.73 %
Rwork0.1999 --
obs0.2009 71350 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.84 Å2 / Biso mean: 50.2465 Å2 / Biso min: 15.91 Å2
Refinement stepCycle: final / Resolution: 1.8→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 772 82 106 2890
Biso mean--40.42 35.97 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072860
X-RAY DIFFRACTIONf_angle_d0.8244032
X-RAY DIFFRACTIONf_chiral_restr0.053433
X-RAY DIFFRACTIONf_plane_restr0.006381
X-RAY DIFFRACTIONf_dihedral_angle_d22.3171539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83270.33683400.301334153755
1.8327-1.868100000000.26433749
1.868-1.90610.26391800.245335553735
1.9061-1.94760.28441460.222336173763
1.9476-1.9929100000000.21273761
1.9929-2.04270.25733040.204134563760
2.0427-2.0979100000000.19773760
2.0979-2.15970.2162690.196934883757
2.1597-2.2294100000000.18723763
2.2294-2.3090.23822550.200134813736
2.309-2.4015100000000.20073751
2.4015-2.51070.25732010.20835643765
2.5107-2.64310.24181970.222635523749
2.6431-2.80860.3833230.21337383761
2.8086-3.02540.24061310.221536243755
3.0254-3.32970.27381380.203136213759
3.3297-3.8110.19972190.181235453764
3.811-4.79990.17071280.165836103738
4.7999-37.12210.22851300.202836393769
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4566-0.1494-0.89662.38790.01383.5022-0.186-0.0724-0.13330.0952-0.015-0.13340.09530.16860.16450.17470.01530.02720.157-0.00240.165132.8921-26.6351-4.9496
22.9284-0.9418-0.82752.32010.4163.4991-0.0258-0.0359-0.03940.1564-0.0010.2042-0.0567-0.0975-0.00360.20660.00810.0430.151-0.00180.227815.9558-12.24842.3396
30.0103-0.12130.00823.68090.78530.3632-0.5339-0.0394-0.0864-0.63410.2981.11110.3693-0.883-0.24020.528-0.37280.14291.0199-0.16410.87033.1785-30.2804-28.3216
42.74413.15710.03973.7439-0.16290.39050.1310.0899-0.03390.14160.3651.32530.3048-0.8164-0.56980.6149-0.35420.11581.1419-0.18321.45682.6532-30.5593-26.8582
53.75813.27620.02153.1942-0.08850.12070.1743-0.02850.3942-0.15830.1758-0.1090.0838-0.1166-0.33141.0937-0.55810.20111.2053-0.21842.0255-27.4137-55.3612-29.6477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA216 - 346
2X-RAY DIFFRACTION2chain BB217 - 350
3X-RAY DIFFRACTION3chain WW1 - 12
4X-RAY DIFFRACTION4chain XX1 - 12
5X-RAY DIFFRACTION5chain YY1 - 12

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