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- PDB-1a1h: QGSR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE) -

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Basic information

Entry
Database: PDB / ID: 1a1h
TitleQGSR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCAC SITE)
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*GP*CP*CP*CP*AP*CP*GP*C)-3')
  • QGSR ZINC FINGER PEPTIDE
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 / response to glucose / BMP signaling pathway / estrous cycle / positive regulation of chemokine production / regulation of neuron apoptotic process / response to ischemia / positive regulation of interleukin-1 beta production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / circadian regulation of gene expression / cellular response to gamma radiation / negative regulation of canonical Wnt signaling pathway / response to insulin / 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 / MIR / Resolution: 1.6 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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*CP*AP*C)-3')
C: DNA (5'-D(*TP*GP*TP*GP*CP*CP*CP*AP*CP*GP*C)-3')
A: QGSR ZINC FINGER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6306
Polymers17,4343
Non-polymers1963
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.100, 55.900, 130.500
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*CP*AP*C)-3')


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


Mass: 3310.161 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein QGSR ZINC FINGER PEPTIDE


Mass: 10724.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PQGSR / 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.: 149 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: 27.5-35% PEG 3350, 0-200 MM NACL, 100 MM TRIS PH 8.5, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACL11
3MES11
4PRECIPITATING SOLUTION11
5WATER12
6NACL12
7TRIS12
8PEG 33501
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
413.25-17.5 %PEG33501drop
550 mMTris-HCl1drop
627.5-35 %PEG33501reservoir
70-200 mM1reservoirNaCl
8100 mMTris-HCl1reservoir

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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, 1995 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 20835 / % possible obs: 95.7 % / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rsym value: 0.035 / Net I/σ(I): 45.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4 / Rsym value: 0.147 / % possible all: 87.8
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % possible obs: 95.7 % / Redundancy: 3.9 % / Num. measured all: 80360 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / % possible obs: 87.8 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2368 11.4 %BASED
Rwork0.235 ---
obs0.235 20810 95.7 %-
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--4.95 Å20 Å2
3---3.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 445 3 149 1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
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_deg0.09
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.8021.5
X-RAY DIFFRACTIONx_mcangle_it1.422
X-RAY DIFFRACTIONx_scbond_it1.382
X-RAY DIFFRACTIONx_scangle_it2.422.5
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.335 292 12.3 %
Rwork0.332 2077 -
obs--87 %
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: 1.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 11.4 % / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27
LS refinement shell
*PLUS
Rfactor obs: 0.332

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