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- PDB-3irr: Crystal Structure of a Z-Z junction (with HEPES intercalating) -

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Basic information

Entry
Database: PDB / ID: 3irr
TitleCrystal Structure of a Z-Z junction (with HEPES intercalating)
Components
  • DNA (5'-D(*A*CP*CP*GP*CP*GP*CP*GP*AP*CP*GP*CP*GP*CP*G)-3')
  • DNA (5'-D(*G*TP*CP*GP*CP*GP*CP*GP*TP*CP*GP*CP*GP*CP*G)-3')
  • Double-stranded RNA-specific adenosine deaminase
KeywordsHYDROLASE/DNA / Z-DNA / ADAR1 / RNA EDITING / INNATE IMMUNITY / DNA JUNCTION / Z DOMAIN / INTERCALATION / Alternative promoter usage / Alternative splicing / Cytoplasm / Disease mutation / DNA-binding / Hydrolase / Isopeptide bond / Metal-binding / mRNA processing / Nucleus / Phosphoprotein / Polymorphism / RNA-binding / RNA-mediated gene silencing / Ubl conjugation / Zinc / HYDROLASE-DNA COMPLEX
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 / hematopoietic progenitor cell differentiation / RNA processing / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / mRNA processing / cellular response to virus / osteoblast differentiation / protein import into nucleus / double-stranded RNA binding / Interferon alpha/beta signaling / 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 / DNA (> 10) / Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsAthanasiadis, A. / de Rosa, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of a junction between two Z-DNA helices.
Authors: de Rosa, M. / de Sanctis, D. / Rosario, A.L. / Archer, M. / Rich, A. / Athanasiadis, A. / Carrondo, M.A.
History
DepositionAug 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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
A: Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-specific adenosine deaminase
C: Double-stranded RNA-specific adenosine deaminase
F: DNA (5'-D(*G*TP*CP*GP*CP*GP*CP*GP*TP*CP*GP*CP*GP*CP*G)-3')
G: DNA (5'-D(*A*CP*CP*GP*CP*GP*CP*GP*AP*CP*GP*CP*GP*CP*G)-3')
D: Double-stranded RNA-specific adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9137
Polymers38,6746
Non-polymers2381
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.667, 102.205, 105.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a double stranded DNA molecule bound by four protein molecules

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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: 7372.584 Da / Num. of mol.: 4 / Fragment: Zalpha domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR, ADAR1, DSRAD, G1P1, IFI4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P55265, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA (5'-D(*G*TP*CP*GP*CP*GP*CP*GP*TP*CP*GP*CP*GP*CP*G)-3')


Mass: 4602.959 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*A*CP*CP*GP*CP*GP*CP*GP*AP*CP*GP*CP*GP*CP*G)-3')


Mass: 4580.963 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 2000 MME, 0.1 M HEPES, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.65→47.04 Å / Num. all: 10248 / Num. obs: 10230 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 64.54 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.049 / Net I/σ(I): 12.2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1488 / Rsym value: 0.294 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QBJ

1qbj


Resolution: 2.65→46.023 Å / SU ML: 0.39 / σ(F): 1.36 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 491 4.83 %RANDOM
Rwork0.2294 ---
all0.232 10166 --
obs0.2294 10166 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.41 Å2 / ksol: 0.324 e/Å3
Refinement stepCycle: LAST / Resolution: 2.65→46.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 545 15 32 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022597
X-RAY DIFFRACTIONf_angle_d0.5113597
X-RAY DIFFRACTIONf_dihedral_angle_d18.5911037
X-RAY DIFFRACTIONf_chiral_restr0.027401
X-RAY DIFFRACTIONf_plane_restr0.003353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.91670.38951180.29832366X-RAY DIFFRACTION100
2.9167-3.33870.33511330.25372393X-RAY DIFFRACTION99
3.3387-4.20590.27181200.19682408X-RAY DIFFRACTION99
4.2059-46.02960.22721200.20342508X-RAY DIFFRACTION97

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