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- PDB-3f21: Crystal structure of Zalpha in complex with d(CACGTG) -

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Basic information

Entry
Database: PDB / ID: 3f21
TitleCrystal structure of Zalpha in complex with d(CACGTG)
Components
  • DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')
  • Double-stranded RNA-specific adenosine deaminase
KeywordsHYDROLASE / Protein-Z-DNA complex / Alternative promoter usage / Alternative splicing / Cytoplasm / Disease mutation / DNA-binding / Metal-binding / mRNA processing / Nucleus / Phosphoprotein / Polymorphism / RNA-binding / RNA-mediated gene silencing / Ubl conjugation / Zinc
Function / homology
Function and homology information


somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / hematopoietic stem cell homeostasis / response to interferon-alpha / adenosine to inosine editing / RISC complex assembly / pre-miRNA processing / negative regulation of hepatocyte apoptotic process / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / RNA processing / hematopoietic progenitor cell differentiation / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / mRNA processing / osteoblast differentiation / cellular response to virus / protein import into nucleus / Interferon alpha/beta signaling / double-stranded RNA binding / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Z-binding domain profile. / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Z-binding domain / Adenosine deaminase z-alpha domain ...ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Z-binding domain profile. / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Z-binding domain / Adenosine deaminase z-alpha domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHa, S.C. / Choi, J. / Kim, K.K.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ{alpha}ADAR1
Authors: Ha, S.C. / Choi, J. / Hwang, H.Y. / Rich, A. / Kim, Y.G. / Kim, K.K.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 7, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-specific adenosine deaminase
C: Double-stranded RNA-specific adenosine deaminase
D: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')
E: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')
F: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)33,3476
Polymers33,3476
Non-polymers00
Water3,657203
1
A: Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-specific adenosine deaminase
D: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')
E: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)22,2314
Polymers22,2314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-20 kcal/mol
Surface area9870 Å2
MethodPISA
2
C: Double-stranded RNA-specific adenosine deaminase
F: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')

C: Double-stranded RNA-specific adenosine deaminase
F: DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)22,2314
Polymers22,2314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2240 Å2
ΔGint-20 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.365, 87.365, 72.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-227-

HOH

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Components

#1: Protein Double-stranded RNA-specific adenosine deaminase / DRADA / 136 kDa double-stranded RNA-binding protein / P136 / K88DSRBP / Interferon-inducible protein 4 / IFI-4


Mass: 9002.293 Da / Num. of mol.: 3 / Fragment: N-terminal zalpha Domain, UNP residues 133-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P55265, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')


Mass: 2113.410 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2Glycerol11
3HOH11
4(NH4)2SO412
5Glycerol12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 14901 / Num. obs: 14216 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rsym value: 0.038 / Net I/σ(I): 38.9
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.286 / % possible all: 98

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBJ

1qbj


Resolution: 2.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 686 -RAMDOM
Rwork0.238 ---
all-14826 --
obs-13692 92.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 369 0 203 2099

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