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- PDB-5tdr: Set3 PHD finger in complex with histone H3K4me2 -

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Basic information

Entry
Database: PDB / ID: 5tdr
TitleSet3 PHD finger in complex with histone H3K4me2
Components
  • Histone H3
  • SET domain-containing protein 3
KeywordsTRANSCRIPTION / epigenetics / methylation / histone
Function / homology
Function and homology information


Set3 complex / negative regulation of meiotic nuclear division / Rpd3L-Expanded complex / Chromatin modifying enzymes / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / transcription initiation-coupled chromatin remodeling / Assembly of the ORC complex at the origin of replication ...Set3 complex / negative regulation of meiotic nuclear division / Rpd3L-Expanded complex / Chromatin modifying enzymes / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / transcription initiation-coupled chromatin remodeling / 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) / HCMV Late Events / cellular response to starvation / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / epigenetic regulation of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / meiotic cell cycle / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA damage response / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / metal ion binding
Similarity search - Function
Set3/4, SET domain / PhD finger domain / 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 / Zinc finger, PHD-type, conserved site ...Set3/4, SET domain / PhD finger domain / 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 / Zinc finger, PHD-type, conserved site / PHD-finger / 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. / Zinc finger, FYVE/PHD-type / 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
SET domain-containing protein 3 / Histone H3.1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å
AuthorsAndrews, F.H. / Ali, M. / Kutateladze, T.G.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Insight into Recognition of Methylated Histone H3K4 by Set3.
Authors: Gatchalian, J. / Ali, M. / Andrews, F.H. / Zhang, Y. / Barrett, A.S. / Kutateladze, T.G.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SET domain-containing protein 3
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4966
Polymers9,3202
Non-polymers1774
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-23 kcal/mol
Surface area5630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.931, 43.720, 84.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

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Components

#1: Protein SET domain-containing protein 3


Mass: 8041.148 Da / Num. of mol.: 1 / Fragment: unp residues 116-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SET3, YKR029C / Production host: Escherichia coli (E. coli) / References: UniProt: P36124
#2: Protein/peptide Histone H3


Mass: 1278.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 20% PEG3350, 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→38.86 Å / Num. obs: 18587 / % possible obs: 98.4 % / Redundancy: 3.5 % / Net I/σ(I): 7.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.42→38.85 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 929 5 %
Rwork0.1528 --
obs0.1552 18586 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 4 201 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005671
X-RAY DIFFRACTIONf_angle_d0.893904
X-RAY DIFFRACTIONf_dihedral_angle_d13.374261
X-RAY DIFFRACTIONf_chiral_restr0.03999
X-RAY DIFFRACTIONf_plane_restr0.003120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.49490.28581180.2172227X-RAY DIFFRACTION89
1.4949-1.58850.19721310.17022501X-RAY DIFFRACTION100
1.5885-1.71120.20891330.14862529X-RAY DIFFRACTION100
1.7112-1.88340.20951350.14142558X-RAY DIFFRACTION100
1.8834-2.15590.18141330.12922541X-RAY DIFFRACTION100
2.1559-2.71610.17211360.14722580X-RAY DIFFRACTION100
2.7161-38.86410.2061430.15742721X-RAY DIFFRACTION100

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