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

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Basic information

Entry
Database: PDB / ID: 4gne
TitleCrystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
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 / histone H3 methyltransferase activity / oocyte maturation / nucleus organization / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / 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 / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / 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 / osteoblast differentiation / male gonad development / 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 / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / methylation / cell population proliferation / chromosome, telomeric region / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / : / : / 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 ...: / : / : / : / : / : / 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. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Zinc/RING finger domain, C3HC4 (zinc finger) / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / 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 / SAD / Resolution: 1.47 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0976
Polymers12,8362
Non-polymers2624
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-11 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 57.200, 107.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1709-

HOH

21A-1716-

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: 776.881 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-8 / 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.: 136 / 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 Å3/Da / Density % sol: 38.54 % / Mosaicity: 0.21 °
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCl pH 7.0, 30% (w/v) PEG 3000, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionRedundancy: 39.7 % / Av σ(I) over netI: 4.6 / Number: 733354 / Rsym value: 0.085 / D res high: 1.465 Å / D res low: 49.536 Å / Num. obs: 18490 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
4.6336.4296.910.0660.06633.1
3.284.6399.610.0680.06835.3
2.673.2810010.090.0938.3
2.322.6710010.0820.08239.5
2.072.3210010.0780.07840.6
1.892.0710010.0950.09540.9
1.751.8999.910.1050.10541.3
1.641.7599.710.1310.13141.6
1.541.6499.610.1920.19241.7
1.471.5498.510.2810.28137.4
ReflectionResolution: 1.465→49.536 Å / Num. all: 18583 / Num. obs: 18490 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 39.7 % / Rsym value: 0.085 / Net I/σ(I): 36.7
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
1.47-1.5437.40.2930.2812.69698725930.0470.2930.28115.498.5
1.54-1.6441.70.2030.1923.710340724810.0310.2030.19222.199.6
1.64-1.7541.60.1410.1315.39741123440.0220.1410.13129.499.7
1.75-1.8941.30.1160.1056.29144922150.0180.1160.10535.799.9
1.89-2.0740.90.1060.0956.78368820450.0160.1060.09541.7100
2.07-2.3240.60.0870.0787.77586118670.0130.0870.07848.2100
2.32-2.6739.50.0910.0827.16618616740.0140.0910.08249.9100
2.67-3.2838.30.0970.096.55531214440.0150.0970.0953.8100
3.28-4.6335.30.0740.0688.34032411410.0120.0740.06855.599.6
4.63-36.41733.10.0760.0668.8227296860.0130.0760.06651.196.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→36.42 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1548 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9132 / SU B: 1.663 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0728 / SU Rfree: 0.0637 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 948 5.1 %RANDOM
Rwork0.148 ---
obs0.1495 18455 99.3 %-
all-18583 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.93 Å2 / Biso mean: 19.2855 Å2 / Biso min: 8.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.47→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 4 136 950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02889
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9541211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06725.12241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58715146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.026152
X-RAY DIFFRACTIONr_chiral_restr0.0880.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021706
X-RAY DIFFRACTIONr_rigid_bond_restr1.773887
X-RAY DIFFRACTIONr_sphericity_bonded11.5695862
LS refinement shellResolution: 1.465→1.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 65 -
Rwork0.161 1239 -
all-1304 -
obs--97.02 %

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