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- PDB-1a1k: RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE) -

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Basic information

Entry
Database: PDB / ID: 1a1k
TitleRADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE)
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3')
  • RADR ZIF268 VARIANT
KeywordsTRANSCRIPTION/DNA / COMPLEX (ZINC FINGER-DNA) / ZINC FINGER / DNA-BINDING PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / 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 ...regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / 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 / locomotor rhythm / skeletal muscle cell differentiation / T cell differentiation / BMP signaling pathway / response to glucose / estrous cycle / positive regulation of chemokine production / regulation of neuron apoptotic process / positive regulation of interleukin-1 beta production / response to ischemia / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to insulin / promoter-specific chromatin binding / circadian regulation of gene expression / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / ISOMORPHOUS MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsElrod-Erickson, M. / Benson, T.E. / Pabo, C.O.
Citation
Journal: Structure / Year: 1998
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: 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: Science / Year: 1994
Title: Zinc Finger Phage: Affinity Selection of Fingers with New DNA-Binding Specificities
Authors: Rebar, E.J. / Pabo, C.O.
#3: 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
DepositionDec 10, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 10, 1998Provider: 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_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

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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*AP*CP*C)-3')
C: DNA (5'-D(*TP*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3')
A: RADR ZIF268 VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7016
Polymers17,5053
Non-polymers1963
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.700, 55.500, 130.400
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 DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3')


Mass: 3399.223 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3310.161 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein RADR ZIF268 VARIANT


Mass: 10795.463 Da / Num. of mol.: 1 / Fragment: ZINC FINGER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PRADR / 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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growpH: 6.2 / Details: 25% PEG 1450, 25 MM MES PH 6.2
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACL11
3MES11
4PEG 335011
5WATER12
6NACL12
7MES12
8PEG 335012
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMzinc-finger-DNA complex1drop
2150 mM1dropNaCl
325 mM1drop
412.5 %PEG14501drop
525 %PEG14501reservoir
675 mMMES1reservoir
71
81

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 23142 / % possible obs: 79.9 % / Observed criterion σ(I): -2 / Redundancy: 2.3 % / Rsym value: 0.034 / Net I/σ(I): 24.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.258 / % possible all: 63.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 79.9 % / Redundancy: 2.3 % / Num. measured all: 10102 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 63.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAY, WITHOUT WATERS AND WITHOUT SIDE CHAINS FOR RESIDUES 18 - 24

1aay


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1079 10.9 %BASED
Rwork0.21 ---
obs0.21 9890 78.5 %-
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.729 Å20 Å20 Å2
2--9.654 Å20 Å2
3---4.526 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 445 3 121 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
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_deg1.14
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.821.5
X-RAY DIFFRACTIONx_mcangle_it1.4492
X-RAY DIFFRACTIONx_scbond_it1.3952
X-RAY DIFFRACTIONx_scangle_it2.3852.5
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.323 119 13.3 %
Rwork0.33 773 -
obs--58.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNATOPNDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor obs: 0.33

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