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- PDB-4m9e: Structure of Klf4 zinc finger DNA binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4m9e
TitleStructure of Klf4 zinc finger DNA binding domain in complex with methylated DNA
Components
  • DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3')
  • Krueppel-like factor 4
KeywordsTRANSCRIPTION/DNA / DNA methylation / transcription factor / cellular reprogramming / C2H2 Zinc finger / DNA binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of leukocyte adhesion to arterial endothelial cell / regulation of blastocyst development / cellular response to cycloheximide / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of response to cytokine stimulus / positive regulation of hemoglobin biosynthetic process / post-embryonic camera-type eye development / glandular epithelial cell differentiation / epidermal cell differentiation ...negative regulation of leukocyte adhesion to arterial endothelial cell / regulation of blastocyst development / cellular response to cycloheximide / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of response to cytokine stimulus / positive regulation of hemoglobin biosynthetic process / post-embryonic camera-type eye development / glandular epithelial cell differentiation / epidermal cell differentiation / negative regulation of heterotypic cell-cell adhesion / epidermis morphogenesis / cellular response to peptide / regulation of axon regeneration / cellular response to laminar fluid shear stress / negative regulation of interleukin-8 production / post-embryonic hemopoiesis / negative regulation of cell migration involved in sprouting angiogenesis / defense response to tumor cell / stem cell population maintenance / lncRNA binding / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of sprouting angiogenesis / fat cell differentiation / positive regulation of telomere maintenance / regulation of cell differentiation / somatic stem cell population maintenance / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / epidermis development / establishment of skin barrier / canonical Wnt signaling pathway / response to retinoic acid / cellular response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / cellular response to leukemia inhibitory factor / negative regulation of angiogenesis / negative regulation of cell migration / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / euchromatin / cellular response to growth factor stimulus / beta-catenin binding / chromatin DNA binding / positive regulation of miRNA transcription / cellular response to hydrogen peroxide / histone deacetylase binding / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / microtubule cytoskeleton / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of gene expression / 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 / cytosol / cytoplasm
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
ACETATE ION / DNA / Krueppel-like factor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsLiu, Y. / Olanrewaju, Y.O. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural basis for Klf4 recognition of methylated DNA.
Authors: Liu, Y. / Olanrewaju, Y.O. / Zheng, Y. / Hashimoto, H. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Sep 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_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Krueppel-like factor 4
B: DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8968
Polymers16,5493
Non-polymers3475
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-5 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.705, 48.705, 131.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Krueppel-like factor 4 / Epithelial zinc finger protein EZF / Gut-enriched krueppel-like factor


Mass: 10428.806 Da / Num. of mol.: 1 / Fragment: UNP residues 396-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klf4, Ezf, Gklf, Zie / Plasmid: pXC1248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60793

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3')


Mass: 3140.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis
#3: DNA chain DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3')


Mass: 2979.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis

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Non-polymers , 4 types, 139 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.25M NaCl and 20% polyethylene glycol 8000, pH 8.5, 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: Apr 3, 2013
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liqued nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→70 Å / Num. obs: 13918 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 27.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1103 / % possible all: 80.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WBU

2wbu


Resolution: 1.851→34.44 Å / SU ML: 0.18 / Isotropic thermal model: FLAT BULK SOLVENT MODEL / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 689 4.98 %RANDOM
Rwork0.1868 ---
obs0.1889 13843 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.851→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 406 13 134 1247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061230
X-RAY DIFFRACTIONf_angle_d1.3131753
X-RAY DIFFRACTIONf_dihedral_angle_d26.221512
X-RAY DIFFRACTIONf_chiral_restr0.063166
X-RAY DIFFRACTIONf_plane_restr0.005147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.851-1.99390.27681360.23452296229689
1.9939-2.19460.24771330.197826382638100
2.1946-2.5120.22971460.19426512651100
2.512-3.16450.30471430.209426972697100
3.1645-34.44560.18731310.16482872287299
Refinement TLS params.Method: refined / Origin x: 53.3137 Å / Origin y: 72.266 Å / Origin z: 141.9154 Å
111213212223313233
T0.123 Å2-0.0184 Å20.0158 Å2-0.1368 Å20.0155 Å2--0.0927 Å2
L1.5052 °2-0.8003 °2-0.2145 °2-1.6636 °20.7061 °2--1.1247 °2
S0.0111 Å °0.0839 Å °0.0685 Å °0.0487 Å °0.0233 Å °-0.0075 Å °0.0555 Å °-0.1108 Å °-0.0315 Å °
Refinement TLS groupSelection details: all

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