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- PDB-5ke7: mouse Klf4 ZnF1-3 and TpG/MpA sequence DNA complex structure -

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Basic information

Entry
Database: PDB / ID: 5ke7
Titlemouse Klf4 ZnF1-3 and TpG/MpA 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*(5CM)P*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: 2.06 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 ...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: 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*(5CM)P*AP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,39010
Polymers16,9453
Non-polymers4447
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint11 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 50.750, 130.390
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: 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

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DNA chain , 2 types, 2 molecules BC

#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*(5CM)P*AP*CP*CP*TP*C)-3')


Mass: 2963.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 78 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
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: 2.06→34.6041 Å / Num. obs: 11180 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / CC1/2: 0.922 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.12
Reflection shellResolution: 2.06→2.11 Å / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2376: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M9E

4m9e


Resolution: 2.06→34.599 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 22.9
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 557 4.99 %Random
Rwork0.1932 ---
obs0.1944 11161 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→34.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 405 19 71 1214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031208
X-RAY DIFFRACTIONf_angle_d0.6591701
X-RAY DIFFRACTIONf_dihedral_angle_d24.392626
X-RAY DIFFRACTIONf_chiral_restr0.035172
X-RAY DIFFRACTIONf_plane_restr0.003147
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0602-2.26750.29921350.24632566100
2.2675-2.59550.23181370.21052605100
2.5955-3.26970.24461390.20192637100
3.2697-34.5990.18431460.1738279699
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)
13.735-3.29961.76463.1077-1.4492.2598-0.02811.22280.6022-0.0031-0.3387-0.96270.08670.8588-0.08910.3247-0.1162-0.03990.82770.06080.37137.8569-13.6343-2.394
23.7142-1.4344-0.15743.37810.05783.0967-0.13450.48590.5413-0.14080.0756-0.1664-0.2870.43770.05170.3315-0.1006-0.08620.39620.08280.3821-0.814-11.2432.271
36.85712.85310.63062.82112.60123.6026-0.35470.2372-0.1459-0.2045-0.01240.7964-0.43470.1511-0.0030.32210.0239-0.09690.29850.05160.3126-13.5949-15.56474.533
44.40824.206-5.54664.0499-5.36237.1117-0.0370.55870.1353-0.13250.34160.99240.0034-0.5777-0.14380.3221-0.0264-0.05250.35980.05650.392-23.3594-24.27259.7757
53.8714-0.0311-0.18792.07450.17132.0831-0.0033-0.00880.09750.30630.0387-0.0194-0.2375-0.0972-0.05170.26010.0071-0.00540.26610.05460.2537-14.8146-23.885211.9945
64.6364-3.5236-0.23733.54811.39741.71430.13110.1208-0.70660.11590.0781-0.1190.31150.3176-0.00880.3991-0.0002-0.04020.20270.09610.4138-10.9109-36.523516.8766
71.21462.38860.91357.458-0.07852.1240.0055-0.6051-0.90090.45920.36020.88920.0629-0.0105-0.320.3720.12070.01150.34460.08660.5507-3.1369-44.359622.3213
82.43661.5971-1.08296.5691-5.2864.3066-0.30150.0819-0.41590.05240.29910.39490.068-0.1971-0.13340.36860.09390.02780.28660.11360.4818-6.7874-36.333121.8942
97.4944-6.06037.18376.2471-7.34819.1171-0.609-0.9397-0.03390.86660.5423-0.5214-0.0279-0.26710.10280.42710.06210.02160.35080.02240.38951.9186-36.581422.9995
100.41310.43880.36121.3295-0.0892.1923-0.06880.08990.00230.19120.13920.13310.04610.1884-0.08370.3120.0254-0.02440.32380.03950.2441-0.8949-23.999810.2657
111.5267-0.27621.22831.50120.63233.25280.10830.144-0.15120.14910.1629-0.05560.32520.1045-0.34970.2976-0.0136-0.02890.3099-0.00890.2551-0.5461-25.541911.1481
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 425 )
3X-RAY DIFFRACTION3chain 'A' and (resid 426 through 430 )
4X-RAY DIFFRACTION4chain 'A' and (resid 431 through 435 )
5X-RAY DIFFRACTION5chain 'A' and (resid 436 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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