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- PDB-1jk2: Zif268 D20A mutant bound to the GCT DNA site -

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Basic information

Entry
Database: PDB / ID: 1jk2
TitleZif268 D20A mutant bound to the GCT DNA site
Components
  • 5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3'
  • 5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3'
  • ZIF268
KeywordsTRANSCRIPTION/DNA / zinc-finger / double stranded DNA / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to mycophenolic acid / cellular response to heparin / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to mycophenolic acid / cellular response to heparin / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / : / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / long-term memory / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / regulation of long-term neuronal synaptic plasticity / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of neuron apoptotic process / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / learning or memory / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / 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 / DNA (> 10) / Early growth response protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMiller, J.C. / Pabo, C.O.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition.
Authors: Miller, J.C. / Pabo, C.O.
#1: Journal: Structure / Year: 1996
Title: Zif268 Protein-DNA Complex Refined at 1.6 A: A Model System for Understanding Zinc Finger-DNA Interactions
Authors: Elrod-Erickson, M. / Rould, M.A. / Nekludova, L. / Pabo, C.O.
#2: Journal: J.Biol.Chem. / Year: 1999
Title: Binding Studies with Mutants of Zif268. Contribution of Individual Side Chains to Binding Affinity and Specificity in the Zif268 Zinc Finger-DNA Complex
Authors: Elrod-Erickson, M. / Pabo, C.O.
History
DepositionJul 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3'
C: 5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3'
A: ZIF268
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7156
Polymers17,5193
Non-polymers1963
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.600, 56.050, 131.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 3430.233 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3'


Mass: 3279.151 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein ZIF268 / EARLY GROWTH RESPONSE PROTEIN 1


Mass: 10809.488 Da / Num. of mol.: 1 / Fragment: ZINC FINGERS (Residues 333-421) / Mutation: D120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pZifD20A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P08046
#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 / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 300 mM NaCl, 10% PEG 1450, 25 mM Bis-Tris propane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG145011
2Bis-Tris Propane11
3NaClSodium chloride11
Crystal grow
*PLUS
pH: 6.2 / Details: Elrod-Erickson, M., (1998) Structure, 6,451.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1200 mM1dropNaCl
250 mMMES1drop
3500 mM1reservoirNaCl
415 %PEG14501reservoir
525 mMBis-Tris-propane1reservoirpH8.0

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 28, 1999 / Details: Yale mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 18149 / Num. obs: 18149 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.65→1.71 Å / Num. unique all: 1460 / % possible all: 75.1
Reflection
*PLUS
Num. measured all: 138650
Reflection shell
*PLUS
% possible obs: 75.1 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D20A bound to the wt site with the appropriate change to the DNA and with waters and side chains of residues 18 and 21 removed

Resolution: 1.65→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: X-PLOR parameters PARHCSDX.PRO and PARNDBX.DNA
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1714 9.9 %RANDOM
Rwork0.23 ---
all0.23 18149 --
obs0.23 17401 87.7 %-
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 481 3 145 1377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_improper_angle_d1.41
X-RAY DIFFRACTIONx_mcbond_it0.971.5
X-RAY DIFFRACTIONx_mcangle_it1.692
X-RAY DIFFRACTIONx_scbond_it1.132
X-RAY DIFFRACTIONx_scangle_it1.932.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 215 10 %
Rwork0.395 1935 -
obs--65.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNATOPNDBX.DNA
X-RAY DIFFRACTION3PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.41
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.434 / % reflection Rfree: 10 % / Rfactor Rwork: 0.395

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