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- PDB-1aay: ZIF268 ZINC FINGER-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1aay
TitleZIF268 ZINC FINGER-DNA COMPLEX
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3')
  • DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')
  • PROTEIN (ZIF268 ZINC FINGER PEPTIDE)
KeywordsTRANSCRIPTION/DNA / ZINC FINGER / DNA-BINDING PROTEIN / COMPLEX (ZINC FINGER-DNA) / 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 / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / cellular response to organic substance / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / estrous cycle / T cell differentiation / long-term memory / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / 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 / regulation of long-term neuronal synaptic plasticity / positive regulation of smooth muscle cell proliferation / circadian regulation of gene expression / negative regulation of canonical Wnt signaling pathway / response to insulin / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / response to hypoxia / learning or memory / 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 / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / 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
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: 1.6 Å
AuthorsElrod-Erickson, M. / Rould, M.A. / Pabo, C.O.
Citation
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.
#1: Journal: Science / Year: 1991
Title: Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 A
Authors: Pavletich, N.P. / Pabo, C.O.
History
DepositionJan 18, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_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
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3')
C: DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')
A: PROTEIN (ZIF268 ZINC FINGER PEPTIDE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7596
Polymers17,5633
Non-polymers1963
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.400, 56.200, 130.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-347-

HOH

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Components

#1: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3')


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


Mass: 3279.151 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (ZIF268 ZINC FINGER PEPTIDE)


Mass: 10853.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PZIF89 / 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.: 148 / 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: 2.4 Å3/Da / Density % sol: 55.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 2.5-5% PEG 400; 500-700MM NACL; 25MM BIS-TRIS PROPANE, PH 8.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACLSodium chloride11
3BIS-TRIS-PROPANE_HCL11
4WATER12
5PEG 40012
Crystal grow
*PLUS
Details: Pavletich, N.P., (1991) Science, 252, 809.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMZif complex1drop
2450-750 mM1dropNaCl
3125 mMbis-tris-propane-HCl1drop
40-10 %PEG4001reservoir
5450-650 mM1reservoirNaCl
625 mMbis-tris-propane-HCl1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 22749 / % possible obs: 96.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Rsym value: 0.025 / Net I/σ(I): 34.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2 / Rsym value: 0.223 / % possible all: 92.8
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 27503 / % possible obs: 94.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Num. measured all: 149720 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.534

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZAA, WITHOUT WATERS

1zaa


Resolution: 1.6→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2312 12 %RANDOM
Rwork0.195 ---
all0.203 ---
obs0.195 19207 87 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 445 3 148 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na0.009
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na3.02
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na29.8
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na0.6
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.461
X-RAY DIFFRACTIONx_mcangle_it2.381.5
X-RAY DIFFRACTIONx_scbond_it2.031
X-RAY DIFFRACTIONx_scangle_it3.31.5
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.286 242 12.6 %
Rwork0.266 1674 -
obs--70.1 %
Software
*PLUS
Version: 3.0,3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 12 % / Rfactor all: 0.203 / Rfactor obs: 0.195 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.292
X-RAY DIFFRACTIONx_dihedral_angle_d22.751
X-RAY DIFFRACTIONx_improper_angle_d1.226
X-RAY DIFFRACTIONx_mcbond_it1.461
X-RAY DIFFRACTIONx_scbond_it2.031
X-RAY DIFFRACTIONx_mcangle_it2.381.5
X-RAY DIFFRACTIONx_scangle_it3.31.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / % reflection Rfree: 12.6 % / Rfactor Rwork: 0.266 / Rfactor obs: 0.266

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