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- PDB-4gnf: Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed wit... -

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Basic information

Entry
Database: PDB / ID: 4gnf
TitleCrystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
Components
  • Histone H3.3
  • Histone-lysine N-methyltransferase NSD3
KeywordsTRANSFERASE/NUCLEAR PROTEIN / zinc finger / transcription / histone / nuclear protein / TRANSFERASE-NUCLEAR PROTEIN 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 / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / histone H3K36 methyltransferase activity / pericentric heterochromatin formation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / histone H3K36 methyltransferase activity / pericentric heterochromatin formation / inner kinetochore / transcription regulator activator activity / muscle cell differentiation / oocyte maturation / histone H3 methyltransferase activity / nucleosomal DNA binding / nucleus organization / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / multicellular organism growth / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / methylation / Estrogen-dependent gene expression / chromosome, telomeric region / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / protein-containing complex / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain ...: / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Herpes Virus-1 / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.3 / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsLi, F. / He, C. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition.
Authors: He, C. / Li, F. / Zhang, J. / Wu, J. / Shi, Y.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 NSD3
C: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8866
Polymers13,6252
Non-polymers2624
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 62.710, 62.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1684-

HOH

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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: 12058.793 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1310-1413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WHSC1L1, NSD3, DC28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BZ95, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3.3


Mass: 1565.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-16 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.17 Å3/Da / Density % sol: 43.33 % / Mosaicity: 0.85 °
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97838 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97838 Å / Relative weight: 1
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 6.7 / Number: 118411 / Rsym value: 0.064 / D res high: 1.55 Å / D res low: 44.389 Å / Num. obs: 17540 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
4.931.3593.410.0420.0426.2
3.474.999.810.0390.0396.1
2.833.4710010.0610.0616.3
2.452.8310010.0730.0736.7
2.192.4510010.0810.0816.8
22.1910010.1050.1056.9
1.85210010.140.146.9
1.731.8510010.180.186.9
1.631.7310010.270.276.9
1.551.6310010.4230.4236.9
ReflectionResolution: 1.55→44.389 Å / Num. all: 17558 / Num. obs: 17540 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.064 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.55-1.636.90.4570.4231.81750625310.1730.4570.4233.4100
1.63-1.736.90.2920.272.71669824130.110.2920.275.1100
1.73-1.856.90.1950.183.81562222540.0740.1950.187.5100
1.85-26.90.1520.144.61442620960.0570.1520.1410.3100
2-2.196.90.1140.1055.91324919330.0430.1140.10514100
2.19-2.456.80.0880.0817.41195817650.0340.0880.08117.2100
2.45-2.836.70.0790.0738.21050815750.0310.0790.07320.6100
2.83-3.476.30.0670.0619.5846913460.0270.0670.06125.1100
3.47-4.96.10.0430.03916.3644710550.0170.0430.0393099.8
4.9-31.3556.20.0460.04215.535285720.0180.0460.04228.993.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNE

4gne


Resolution: 1.55→21.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.1672 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8585 / SU B: 3.299 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0826 / SU Rfree: 0.0765 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 890 5.1 %RANDOM
Rwork0.1602 ---
obs0.1625 17533 99.68 %-
all-17558 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.28 Å2 / Biso mean: 30.9116 Å2 / Biso min: 16.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 4 98 917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02856
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9581159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06224.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80215141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.529153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021671
X-RAY DIFFRACTIONr_rigid_bond_restr3.4953855
X-RAY DIFFRACTIONr_sphericity_bonded19.4555834
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 74 -
Rwork0.194 1203 -
all-1277 -
obs--100 %

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