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- PDB-6vtx: Crystal structure of human KLF4 zinc finger DNA binding domain in... -

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Basic information

Entry
Database: PDB / ID: 6vtx
TitleCrystal structure of human KLF4 zinc finger DNA binding domain in complex with NANOG DNA
Components
  • DNA (5'-D(*AP*GP*GP*GP*GP*GP*TP*GP*TP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*AP*CP*AP*CP*CP*CP*CP*CP*T)-3')
  • Krueppel-like factor 4
KeywordsDNA BINDING PROTEIN/DNA / KLF4 / Zinc Finger / DNA binding domain / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


mesodermal cell fate determination / positive regulation of protein metabolic process => GO:0051247 / : / 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 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / positive regulation of hemoglobin biosynthetic process ...mesodermal cell fate determination / positive regulation of protein metabolic process => GO:0051247 / : / 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 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / positive regulation of hemoglobin biosynthetic process / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / epidermal cell differentiation / negative regulation of muscle hyperplasia / FOXO-mediated transcription of cell cycle genes / epidermis morphogenesis / negative regulation of heterotypic cell-cell adhesion / cellular response to peptide / Transcriptional regulation of pluripotent stem cells / positive regulation of core promoter binding / 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 / negative regulation of NF-kappaB transcription factor activity / positive regulation of sprouting angiogenesis / fat cell differentiation / regulation of cell differentiation / somatic stem cell population maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / cis-regulatory region sequence-specific DNA binding / cellular response to retinoic acid / : / positive regulation of protein metabolic process / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / cellular response to growth factor stimulus / positive regulation of miRNA transcription / histone deacetylase binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / cellular response to hydrogen peroxide / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / 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 gene expression / 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 / zinc ion binding / nucleoplasm / 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
DNA / DNA (> 10) / Krueppel-like factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSharma, R. / Sharma, S. / Choi, K.J. / Ferreon, A.C.M. / Ferreon, J.C. / Sankaran, B. / MacKenzie, K.R. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)GM122763 United States
CitationJournal: Nat Commun / Year: 2021
Title: Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization.
Authors: Sharma, R. / Choi, K.J. / Quan, M.D. / Sharma, S. / Sankaran, B. / Park, H. / LaGrone, A. / Kim, J.J. / MacKenzie, K.R. / Ferreon, A.C.M. / Kim, C. / Ferreon, J.C.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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(*AP*GP*GP*GP*GP*GP*TP*GP*TP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*AP*CP*AP*CP*CP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5457
Polymers17,3263
Non-polymers2194
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-37 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.964, 46.688, 45.200
Angle α, β, γ (deg.)90.000, 113.502, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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: 9998.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLF4, EZF, GKLF / Production host: Escherichia coli (E. coli) / References: UniProt: O43474

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3759.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*GP*CP*AP*CP*AP*CP*CP*CP*CP*CP*T)-3')


Mass: 3568.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 85 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: 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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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Sodium iodide (pH 7.0) and 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→41.45 Å / Num. obs: 8237 / % possible obs: 96.14 % / Redundancy: 3.9 % / Biso Wilson estimate: 34.56 Å2 / CC1/2: 0.975 / Net I/σ(I): 4.31
Reflection shellResolution: 2.14→2.21 Å / Num. unique obs: 816 / CC1/2: 0.304

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBU

2wbu


Resolution: 2.14→41.45 Å / SU ML: 0.2702 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 399 4.98 %
Rwork0.217 7617 -
obs0.2184 8016 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.92 Å2
Refinement stepCycle: LAST / Resolution: 2.14→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms656 486 4 81 1227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281223
X-RAY DIFFRACTIONf_angle_d0.40341753
X-RAY DIFFRACTIONf_chiral_restr0.0239183
X-RAY DIFFRACTIONf_plane_restr0.0016142
X-RAY DIFFRACTIONf_dihedral_angle_d25.6083324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.450.3411500.31472365X-RAY DIFFRACTION91.29
2.45-3.090.28781320.26842603X-RAY DIFFRACTION98.88
3.09-41.450.20431170.17762649X-RAY DIFFRACTION98.19
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)
18.610220697781.229092056282.97282861414.64372385504-1.610609166884.70280719359-0.45237191905-1.16432055539-0.3081590726130.4199630994930.278116785308-0.1155321389690.167469312864-0.00930140019152-0.01499253834420.6241229271310.1543702137250.1345902488280.5727841054760.07886703418810.33764187911925.40651588415.8034113762413.2523490596
26.158586203931.34300746042.731550961147.944896755873.54455227194.52367883918-0.5601460415380.7996275780610.245868625392-1.601540513650.2143798591710.0982304843242-1.136910589360.5375070623760.3521404520920.28401205992-0.041237804106-0.03380266269310.2637717550610.09787132630410.26133411189914.6653971198-1.17967634865-3.57292864466
39.175505909784.85351309293-5.427521312576.19952042609-4.336624855768.35465978214-0.168757386747-0.366500329965-0.355353382882-0.0987115098225-0.100712619699-0.1057600930370.53880653488-0.1151079592060.2251738687830.2026426483730.01380900930390.02447044834430.25917744047-0.06019867369150.2245103811286.47032015894-15.73737206055.90890049353
47.68334657704-0.8685669253152.472346128294.15971070115-0.9985484555973.79369439045-0.860267918411-1.475464895310.4041163503060.09311379418850.480762811928-0.2710719364790.03408128390230.02420975939550.1358254639190.2497152637650.1217029754230.06845633587770.561898502741-0.08276854613670.37279335937711.3172980503-7.2347033694910.9393563382
59.558949950060.6582254512891.913406096193.80438261633-0.5350106890913.97724063431-0.415564688504-1.12893158739-0.4458659904280.1899848855670.2013513302730.524833177699-0.303184060585-0.269198818846-0.01752112116830.2244518096470.0323014684639-0.02307237639350.6104993771980.01375861640470.54542170097210.5922790136-6.6311543829810.5797576149
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 430 through 455 )AA430 - 4551 - 26
22chain 'A' and (resid 456 through 473 )AA456 - 47327 - 44
33chain 'A' and (resid 474 through 512 )AA474 - 51245 - 83
44chain 'B' and (resid 1 through 12 )BE1 - 12
55chain 'C' and (resid 1 through 12 )CF1 - 12

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