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Open data
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Basic information
Entry | Database: PDB / ID: 1a1i | ||||||
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Title | RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE) | ||||||
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![]() | TRANSCRIPTION/DNA / ZINC FINGER-DNA COMPLEX / ZINC FINGER / DNA-BINDING PROTEIN / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() 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 heparin / cellular response to mycophenolic acid / 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 heparin / cellular response to mycophenolic acid / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Elrod-Erickson, M. / Benson, T.E. / Pabo, C.O. | ||||||
![]() | ![]() Title: High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Authors: Elrod-Erickson, M. / Benson, T.E. / Pabo, C.O. #1: ![]() 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: ![]() Title: Zinc Finger Phage: Affinity Selection of Fingers with New DNA-Binding Specificities Authors: Rebar, E.J. / Pabo, C.O. #3: ![]() Title: Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 A Authors: Pavletich, N.P. / Pabo, C.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.9 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.2 KB | Display | ![]() |
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Full document | ![]() | 374.3 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a1fC ![]() 1a1gC ![]() 1a1hC ![]() 1a1jC ![]() 1a1kC ![]() 1a1lC ![]() 1aayS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3399.223 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 3310.161 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 10795.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.2 Details: 22.5% PEG 3350, 500MM NACL, 25 MM MES PH 6.2, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 15, 1995 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 21212 / % possible obs: 96.4 % / Observed criterion σ(I): -2 / Redundancy: 2.1 % / Rsym value: 0.049 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 9.2 / Rsym value: 0.109 / % possible all: 89.9 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % possible obs: 96.4 % / Num. measured all: 45579 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 89.9 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 9.2 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AAY, WITHOUT WATERS AND WITHOUT SIDE CHAINS FOR RESIDUES 18 - 24 Resolution: 1.6→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 11.4 % / Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.215 |