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- PDB-2wbs: Crystal structure of the zinc finger domain of Klf4 bound to its ... -

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Basic information

Entry
Database: PDB / ID: 2wbs
TitleCrystal structure of the zinc finger domain of Klf4 bound to its target DNA
Components
  • 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3'
  • 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3'
  • KRUEPPEL-LIKE FACTOR 4
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / DNA-BINDING / TRANSCRIPTION / METAL-BINDING / DNA / PROTEIN / NUCLEUS / ACTIVATOR / ZINC-FINGER / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


negative regulation of leukocyte adhesion to arterial endothelial cell / cellular response to cycloheximide / regulation of blastocyst development / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of hemoglobin biosynthetic process / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / glandular epithelial cell differentiation / epidermal cell differentiation ...negative regulation of leukocyte adhesion to arterial endothelial cell / cellular response to cycloheximide / regulation of blastocyst development / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of hemoglobin biosynthetic process / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / glandular epithelial cell differentiation / epidermal cell differentiation / negative regulation of muscle hyperplasia / epidermis morphogenesis / negative regulation of heterotypic cell-cell adhesion / cellular response to peptide / negative regulation of interleukin-8 production / phosphatidylinositol 3-kinase regulator activity / regulation of axon regeneration / cellular response to laminar fluid shear stress / post-embryonic hemopoiesis / negative regulation of cell migration involved in sprouting angiogenesis / defense response to tumor cell / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / positive regulation of sprouting angiogenesis / fat cell differentiation / regulation of cell differentiation / somatic stem cell population maintenance / epidermis development / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / establishment of skin barrier / cellular response to retinoic acid / response to retinoic acid / negative regulation of angiogenesis / negative regulation of cell migration / : / cellular response to leukemia inhibitory factor / transcription coregulator binding / promoter-specific chromatin binding / negative regulation of smooth muscle cell proliferation / euchromatin / negative regulation of ERK1 and ERK2 cascade / chromatin DNA binding / beta-catenin binding / cellular response to growth factor stimulus / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / microtubule cytoskeleton / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / gene expression / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / 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 / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 / Krueppel-like factor 4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZocher, G. / Schuetz, A. / Carstanjen, D. / Heinemann, U.
CitationJournal: Cell.Mol.Life Sci. / Year: 2011
Title: The Structure of the Klf4 DNA-Binding Domain Links to Self-Renewal and Macrophage Differentiation.
Authors: Schuetz, A. / Nana, D. / Rose, C. / Zocher, G. / Milanovic, M. / Koenigsmann, J. / Blasig, R. / Heinemann, U. / Carstanjen, D.
History
DepositionMar 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 5, 2011Group: Database references / Source and taxonomy
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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_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
F: 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3'
G: 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0847
Polymers14,7963
Non-polymers2884
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.000, 45.970, 73.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein KRUEPPEL-LIKE FACTOR 4 / GUT-ENRICHED KRUEPPEL-LIKE FACTOR / EPITHELIAL ZINC FINGER PROTEIN EZF


Mass: 10557.985 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 395-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: C57BL/6 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q60793

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DNA chain , 2 types, 2 molecules FG

#2: DNA chain 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3' / HEPTAMERIC DNA BINDING SEQUENCE OF KLF4


Mass: 2163.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)
#3: DNA chain 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3' / HEPTAMERIC DNA BINDING SEQUENCE OF KLF4


Mass: 2074.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)

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Non-polymers , 3 types, 135 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGLYCEROL (GOL): CRYO PROTECTANT ZINC ION (ZN): ZINC FINGER MOTIF

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841, 2.0, 1.28204, 1.28312, 1.16967
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 18, 2008 / Details: MIRRORS
RadiationMonochromator: SI111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
221
31.282041
41.283121
51.169671
ReflectionResolution: 1.7→29 Å / Num. obs: 15421 / % possible obs: 97.5 % / Observed criterion σ(I): 2.7 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
XDSdata reduction
XSCALEdata scaling
SHELXSHARP REFMAC5 COOTphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.489 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 770 5 %RANDOM
Rwork0.2 ---
obs0.202 14649 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms716 281 9 131 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211072
X-RAY DIFFRACTIONr_bond_other_d0.0010.02665
X-RAY DIFFRACTIONr_angle_refined_deg1.6442.2431502
X-RAY DIFFRACTIONr_angle_other_deg0.96931603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.681590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53620.97641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11615123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.51158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7586437
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.587697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5167.5635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5787803
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 54 -
Rwork0.285 1026 -
obs--98.18 %
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)
110.9068-2.07446.84883.2251-0.63434.5017-0.3963-0.44280.32290.00350.03790.6784-0.3432-0.35780.35840.17870.1802-0.01320.1986-0.02330.219919.317430.840110.9354
21.8088-0.00620.33090.960.60032.68220.0176-0.0838-0.1243-0.04760.0245-0.0932-0.0469-0.0182-0.04220.0568-0.00720.00350.0351-0.00240.064938.401817.12719.14
30.956-0.6516-1.75960.47981.22173.2531-0.0121-0.1374-0.02280.01210.0259-0.04970.01030.2182-0.01380.0372-0.0181-0.04790.10550.10370.140443.986517.966519.5026
42.2969-0.43082.01261.10780.29132.20490.2112-0.16520.07150.0353-0.2489-0.06950.2099-0.32920.03780.0809-0.0409-0.01120.0920.01210.015438.887618.376720.4086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A397 - 428
2X-RAY DIFFRACTION2A429 - 483
3X-RAY DIFFRACTION3G1 - 7
4X-RAY DIFFRACTION4F1 - 7

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