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- PDB-5xfr: Ternary complex of MTF2, DNA and histone -

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Basic information

Entry
Database: PDB / ID: 5xfr
TitleTernary complex of MTF2, DNA and histone
Components
  • DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
  • Metal-response element-binding transcription factor 2
  • Peptide from Histone H3.1
KeywordsTRANSCRIPTION/DNA / MTF2 / PCL2 / DNA / histone / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


segment specification / ESC/E(Z) complex / stem cell population maintenance / negative regulation of gene expression, epigenetic / Chromatin modifying enzymes / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...segment specification / ESC/E(Z) complex / stem cell population maintenance / negative regulation of gene expression, epigenetic / Chromatin modifying enzymes / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / cellular response to leukemia inhibitory factor / 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 / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / epigenetic regulation of gene expression / transcription corepressor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / stem cell differentiation / 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 / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / metal ion binding / cytoplasm
Similarity search - Function
MTF2, PHD domain 1 / MTF2, PHD domain 2 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / PHD-finger ...MTF2, PHD domain 1 / MTF2, PHD domain 2 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone H3.1 / Metal-response element-binding transcription factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWang, Z. / Li, H.
CitationJournal: Nature / Year: 2017
Title: Polycomb-like proteins link the PRC2 complex to CpG islands
Authors: Li, H. / Liefke, R. / Jiang, J. / Kurland, J.V. / Tian, W. / Deng, P. / Zhang, W. / He, Q. / Patel, D.J. / Bulyk, M.L. / Shi, Y. / Wang, Z.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: 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
Revision 1.2Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Metal-response element-binding transcription factor 2
B: Metal-response element-binding transcription factor 2
C: Peptide from Histone H3.1
D: Peptide from Histone H3.1
E: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
F: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,20114
Polymers82,6786
Non-polymers5238
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-36 kcal/mol
Surface area36350 Å2
Unit cell
Length a, b, c (Å)137.743, 137.743, 101.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Metal-response element-binding transcription factor 2 / Metal regulatory transcription factor 2 / Metal-response element DNA-binding protein M96 / Polycomb- ...Metal regulatory transcription factor 2 / Metal-response element DNA-binding protein M96 / Polycomb-like protein 2 / hPCl2


Mass: 36445.160 Da / Num. of mol.: 2 / Fragment: UNP residues 43-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTF2, PCL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y483
#2: Protein/peptide Peptide from Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 924.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: DNA chain DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')


Mass: 3969.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES monohydrate-pH 6.5, 0.2M ammonium sulfate, 25% PEG monomethyl ether 5000, 10% glycerol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 52840 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 19.6
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 3 / Num. unique all: 3473 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFN

5xfn


Resolution: 2.25→46.593 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.2309 2689 5.1 %
Rwork0.2029 --
obs0.2043 52775 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→46.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 526 8 331 5844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035698
X-RAY DIFFRACTIONf_angle_d0.6347803
X-RAY DIFFRACTIONf_dihedral_angle_d18.0642153
X-RAY DIFFRACTIONf_chiral_restr0.027827
X-RAY DIFFRACTIONf_plane_restr0.002889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2498-2.29070.23731520.22692571X-RAY DIFFRACTION100
2.2907-2.33470.30951490.23282618X-RAY DIFFRACTION100
2.3347-2.38240.26441510.22782584X-RAY DIFFRACTION100
2.3824-2.43420.27621310.23492590X-RAY DIFFRACTION100
2.4342-2.49080.27031160.22262641X-RAY DIFFRACTION100
2.4908-2.55310.21891270.23482661X-RAY DIFFRACTION100
2.5531-2.62210.29321470.23242599X-RAY DIFFRACTION100
2.6221-2.69930.26181330.22662629X-RAY DIFFRACTION100
2.6993-2.78640.26431460.22532614X-RAY DIFFRACTION100
2.7864-2.88590.26111500.2252620X-RAY DIFFRACTION100
2.8859-3.00150.29021320.22532639X-RAY DIFFRACTION100
3.0015-3.13810.26811480.23252625X-RAY DIFFRACTION100
3.1381-3.30350.19921250.21352640X-RAY DIFFRACTION100
3.3035-3.51040.22621390.19982662X-RAY DIFFRACTION100
3.5104-3.78130.21571430.18722639X-RAY DIFFRACTION100
3.7813-4.16160.20261370.17662673X-RAY DIFFRACTION100
4.1616-4.76330.19611620.16562633X-RAY DIFFRACTION100
4.7633-5.99920.20061510.19132699X-RAY DIFFRACTION100
5.9992-46.60260.23231500.19032749X-RAY DIFFRACTION99

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