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- PDB-5ke6: mouse Klf4 ZnF1-3 and TpG/CpA sequence DNA complex structure -

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Basic information

Entry
Database: PDB / ID: 5ke6
Titlemouse Klf4 ZnF1-3 and TpG/CpA sequence DNA complex structure
Components
  • DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*AP*CP*AP*CP*CP*TP*C)-3')
  • Krueppel-like factor 4
Keywordstranscription/DNA / klf4 / zinc finger / Kruppel-like factors / 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 / post-embryonic camera-type eye development / positive regulation of hemoglobin biosynthetic process / negative regulation of muscle hyperplasia / 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 / post-embryonic camera-type eye development / positive regulation of hemoglobin biosynthetic process / negative regulation of muscle hyperplasia / epidermal cell differentiation / negative regulation of heterotypic cell-cell adhesion / epidermis morphogenesis / cellular response to peptide / cellular response to laminar fluid shear stress / phosphatidylinositol 3-kinase regulator activity / negative regulation of interleukin-8 production / regulation of axon regeneration / post-embryonic hemopoiesis / negative regulation of cell migration involved in sprouting angiogenesis / defense response to tumor cell / stem cell population maintenance / negative regulation of G1/S transition of mitotic cell cycle / lncRNA binding / positive regulation of sprouting angiogenesis / fat cell differentiation / positive regulation of telomere maintenance / regulation of cell differentiation / somatic stem cell population maintenance / epidermis development / canonical Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / establishment of skin barrier / response to retinoic acid / cellular response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / epithelial cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cell migration / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / transcription coregulator binding / promoter-specific chromatin binding / negative regulation of smooth muscle cell proliferation / euchromatin / beta-catenin binding / chromatin DNA binding / negative regulation of ERK1 and ERK2 cascade / cellular response to growth factor stimulus / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / microtubule cytoskeleton / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor 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 / cytoplasm / cytosol
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
DNA / Krueppel-like factor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHashimoto, H. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Distinctive Klf4 mutants determine preference for DNA methylation status.
Authors: Hashimoto, H. / Wang, D. / Steves, A.N. / Jin, P. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionJun 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*TP*GP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*CP*AP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1276
Polymers16,9313
Non-polymers1963
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 50.870, 130.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 10840.261 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) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q60793
#2: DNA chain DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3')


Mass: 3141.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*AP*CP*AP*CP*CP*TP*C)-3')


Mass: 2949.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH8.5 , 0.25M NaCl and 20% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→34.678 Å / Num. obs: 12435 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / CC1/2: 0.906 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.58
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.982 / Mean I/σ(I) obs: 2.32

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M9E

4m9e


Resolution: 1.99→34.678 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 622 5.01 %Random
Rwork0.1979 ---
obs0.1997 12416 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→34.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 404 3 81 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081195
X-RAY DIFFRACTIONf_angle_d0.8741674
X-RAY DIFFRACTIONf_dihedral_angle_d25.44614
X-RAY DIFFRACTIONf_chiral_restr0.04170
X-RAY DIFFRACTIONf_plane_restr0.005145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9899-2.19020.29581510.26542867X-RAY DIFFRACTION100
2.1902-2.5070.25361520.22892885X-RAY DIFFRACTION100
2.507-3.15820.27721550.2252948X-RAY DIFFRACTION100
3.1582-34.68330.20261640.173094X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0543-4.379-2.81466.82622.3438.6627-0.13460.65470.6351-0.10780.006-0.681-0.19790.65440.08870.3371-0.11-0.0790.45860.07690.3708-26.316-36.8602262.8873
23.80141.3026-2.99446.0494-1.40237.054-0.0343-0.3633-0.28720.35370.18490.3576-0.012-0.3007-0.21290.2627-0.0184-0.03380.31270.09890.2322-41.7697-49.4253272.1995
33.8323-2.07391.53196.5886-4.54135.3338-0.3637-0.3973-1.00160.55150.69650.94460.0634-0.0862-0.29260.43990.11760.05940.39710.07170.5015-27.6379-63.4492283.0868
41.91330.041-0.10552.1941.88384.0823-0.1080.01750.07970.23410.2808-0.10270.21910.2818-0.17140.31030.0417-0.04880.3580.03610.2026-26.4226-49.4529271.3599
53.76540.31192.26785.48613.4053.8610.01570.2396-0.22810.56050.3569-0.34890.3820.389-0.36130.31-0.0262-0.02090.36060.00570.2425-26.0895-50.9288272.298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 399:427)
2X-RAY DIFFRACTION2(chain A and resid 428:457)
3X-RAY DIFFRACTION3(chain A and resid 458:483)
4X-RAY DIFFRACTION4(chain B and resid 1:10)
5X-RAY DIFFRACTION5(chain C and resid 1:10)

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