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- PDB-5kea: mouse Klf4 ZnF1-3 (E446D) and CpG/CpG sequence DNA complex struct... -

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Basic information

Entry
Database: PDB / ID: 5kea
Titlemouse Klf4 ZnF1-3 (E446D) and CpG/CpG sequence DNA complex structure: Form I
Components
  • DNA (5'-D(*GP*AP*GP*GP*CP*GP*TP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*AP*CP*GP*CP*CP*TP*C)-3')
  • Krueppel-like factor 4
Keywordstranscription factor/DNA / Klf4 / zinc finger / unmethylated cytosine specific / transcription factor-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 / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / canonical Wnt signaling pathway / 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 / negative regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / 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: 2.458 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 1.4Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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*CP*GP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*CP*GP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1146
Polymers16,9183
Non-polymers1963
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-22 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.850, 50.850, 131.050
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: 10826.235 Da / Num. of mol.: 1 / Fragment: unp residues 396-483 / Mutation: E446D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klf4, Ezf, Gklf, Zie / Plasmid: pXC1411 / 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*CP*GP*TP*GP*GP*C)-3')


Mass: 3126.040 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*GP*CP*CP*TP*C)-3')


Mass: 2965.945 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.: 15 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
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-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 11, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→47.7 Å / Num. obs: 6808 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.37
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.03 / % possible all: 7.3

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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: 2.458→47.406 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.32
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 518 10.01 %Random
Rwork0.2289 ---
obs0.2346 5174 76.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.458→47.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 404 3 15 1140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021207
X-RAY DIFFRACTIONf_angle_d0.541690
X-RAY DIFFRACTIONf_dihedral_angle_d23.046458
X-RAY DIFFRACTIONf_chiral_restr0.036173
X-RAY DIFFRACTIONf_plane_restr0.002147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4582-2.70550.5378330.41429220
2.7055-3.09690.36121400.3314126485
3.0969-3.90150.31351660.2318149599
3.9015-47.40.23551790.1913160599
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)
14.62490.1319-0.31544.7898-3.71217.9028-0.1366-0.40390.5489-1.7964-0.6184-0.35920.72681.45970.41120.7477-0.06150.16740.9080.02510.92758.6697-13.6071-7.1851
23.8782-2.9845-2.43555.34091.29711.6368-0.4171-0.44121.4414-0.56271-0.95420.6980.0648-0.17590.863-0.3627-0.1620.82590.09970.90944.5023-4.60891.3813
31.7941-0.9037-1.12563.1872-0.93854.0281-0.13780.05670.594-0.308-0.78080.411-0.46660.8808-1.09650.4595-0.267-0.23430.82250.14930.63897.1643-15.00680.7117
43.30780.4503-1.37893.3435-0.65860.6297-0.17370.52980.5056-0.3068-0.22390.89410.733-0.38490.44310.5734-0.1405-0.0980.546-0.0950.4178-0.7297-13.53340.9822
51.8557-0.4370.40523.8436-1.47491.9085-0.2012-0.0772-0.05-0.14410.35780.14590.1991-0.2926-0.25070.2934-0.0039-0.01690.27870.02850.3038-13.3254-20.90499.787
68.0179-3.4709-1.36483.89260.17341.71540.9258-1.0703-0.44450.6757-0.2672-0.49771.25570.2493-0.59020.6329-0.0706-0.13430.5498-0.17670.6474-10.6538-36.690513.963
70.64540.7357-0.40482.65871.14671.7952-0.4412-0.4138-0.8977-1.60350.97830.21650.73620.4604-0.63410.7885-0.0430.09970.77890.21640.865-3.7851-45.470419.406
81.10811.3002-2.72697.0026-6.09278.26010.267-0.993-0.7371.55160.56511.0362-0.8977-0.0344-0.54950.43750.0815-0.03550.59340.26310.5572-7.0717-37.116118.8289
94.2402-2.35522.73545.0423-2.70725.5683-0.0987-1.13690.40990.22190.556-0.51370.7219-0.3648-0.59920.61090.0952-0.03410.67850.01230.41421.3784-37.551220.9894
100.6619-0.30030.85271.58310.73671.7258-0.04360.1343-0.0023-0.1958-0.04080.2310.36770.47990.0360.38940.0058-0.03040.52830.02010.26020.1957-24.70238.044
110.12460.2380.96222.3960.4234.63070.2790.0494-0.05870.0037-0.0380.08220.7602-0.3471-0.17640.3885-0.03230.02270.7225-0.01230.35990.0937-26.17648.8455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 397 through 401 )
2X-RAY DIFFRACTION2chain 'A' and (resid 402 through 406 )
3X-RAY DIFFRACTION3chain 'A' and (resid 407 through 413 )
4X-RAY DIFFRACTION4chain 'A' and (resid 414 through 424 )
5X-RAY DIFFRACTION5chain 'A' and (resid 425 through 455 )
6X-RAY DIFFRACTION6chain 'A' and (resid 456 through 460 )
7X-RAY DIFFRACTION7chain 'A' and (resid 461 through 465 )
8X-RAY DIFFRACTION8chain 'A' and (resid 466 through 471 )
9X-RAY DIFFRACTION9chain 'A' and (resid 472 through 483 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 10 )

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