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- PDB-4r2c: Egr1/Zif268 zinc fingers in complex with hydroxymethylated DNA -

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Basic information

Entry
Database: PDB / ID: 4r2c
TitleEgr1/Zif268 zinc fingers in complex with hydroxymethylated DNA
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5HC)P*GP*T)-3')
  • DNA (5'-D(*TP*AP*(5HC)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
  • Early growth response protein 1
KeywordsDNA Binding Protein/DNA / Zinc finger / Transcription / DNA Binding Protein-DNA complex
Function / homology
Function and homology information


glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / NGF-stimulated transcription / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / BMP signaling pathway / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / Regulation of PTEN gene transcription / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Early growth response protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X.
CitationJournal: Genes Dev. / Year: 2014
Title: Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Authors: Hashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Sep 20, 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_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_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.pdbx_leaving_atom_flag / _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_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_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: Early growth response protein 1
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5HC)P*GP*T)-3')
C: DNA (5'-D(*TP*AP*(5HC)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1397
Polymers17,9033
Non-polymers2354
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-14 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.977, 56.076, 129.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Early growth response protein 1 / EGR-1 / AT225 / Nerve growth factor-induced protein A / NGFI-A / Transcription factor ETR103 / ...EGR-1 / AT225 / Nerve growth factor-induced protein A / NGFI-A / Transcription factor ETR103 / Transcription factor Zif268 / Zinc finger protein 225 / Zinc finger protein Krox-24


Mass: 11133.757 Da / Num. of mol.: 1 / Fragment: Zinc Finger 1-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGR1, KROX24, ZNF225 / Plasmid: pGEX6p-1, pXC1272 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P18146

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5HC)P*GP*T)-3')


Mass: 3460.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*(5HC)P*GP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3309.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 188 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 0.2 M KCl, 50 mM Hepes-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→28.04 Å / Num. obs: 13248 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 25.25 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 29.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1279 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4R2A

4r2a


Resolution: 1.89→28.038 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 660 5 %RANDOM
Rwork0.1987 ---
all0.2013 13207 --
obs0.2013 13207 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→28.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 449 4 184 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091335
X-RAY DIFFRACTIONf_angle_d0.7871906
X-RAY DIFFRACTIONf_dihedral_angle_d22.675572
X-RAY DIFFRACTIONf_chiral_restr0.037212
X-RAY DIFFRACTIONf_plane_restr0.003159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: 132 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8899-2.03580.32120.258724452577
2.0358-2.24060.2780.224625002632
2.2406-2.56470.24360.21824842616
2.5647-3.23040.2850.206225062638
3.2304-28.04110.20840.171826122744

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