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- PDB-5zuo: Crystal Structure of BZ junction in diverse sequence -

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Basic information

Entry
Database: PDB / ID: 5zuo
TitleCrystal Structure of BZ junction in diverse sequence
Components
  • DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*CP*GP*CP*GP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*AP*AP*AP*CP*C)-3')
  • Double-stranded RNA-specific adenosine deaminase
KeywordsHYDROLASE/DNA / Z-DNA / B-Z junction / protein-DNA complex / 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 / negative regulation of hepatocyte apoptotic process / pre-miRNA processing / 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 / cellular response to virus / osteoblast differentiation / 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 / nucleus / metal ion binding / cytoplasm / cytosol
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.902 Å
AuthorsKim, K.K. / Kim, D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
SSTF-BA1301-01 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Sequence preference and structural heterogeneity of BZ junctions.
Authors: Kim, D. / Hur, J. / Han, J.H. / Ha, S.C. / Shin, D. / Lee, S. / Park, S. / Sugiyama, H. / Kim, K.K.
History
DepositionMay 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Double-stranded RNA-specific adenosine deaminase
E: DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*AP*AP*AP*CP*C)-3')
F: DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*CP*GP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)39,9076
Polymers39,9076
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-55 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.237, 111.237, 62.211
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Double-stranded RNA-specific adenosine deaminase / DRADA / 136 kDa double-stranded RNA-binding protein / p136 / Interferon-inducible protein 4 / IFI-4 / K88DSRBP


Mass: 7372.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR, ADAR1, DSRAD, G1P1, IFI4 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P55265, double-stranded RNA adenine deaminase
#2: DNA chain DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*AP*AP*AP*CP*C)-3')


Mass: 5197.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*CP*GP*CP*GP*CP*GP*CP*G)-3')


Mass: 5219.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.78 Å3/Da / Density % sol: 55.82 % / Mosaicity: 0.739 °
Crystal growTemperature: 296 K / Method: batch mode / pH: 7.5 / Details: 20% dioxane, with microseeding of small crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 9722 / % possible obs: 98.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 96.18 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.917 / Net I/σ(I): 15.3 / Num. measured all: 105614
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.9-2.9511.20.5744850.9511100
2.95-311.20.5274840.9771100
3-3.0611.30.4274871.0231100
3.06-3.1211.30.3024941.0221100
3.12-3.1911.30.274921.1091100
3.19-3.2711.20.1685011.1311100
3.27-3.3511.30.1484701.2061100
3.35-3.4411.30.1124921.2441100
3.44-3.5411.20.0944891.369199.8
3.54-3.6511.20.0834841.4471100
3.65-3.7811.10.0794871.8011100
3.78-3.9411.10.074881.7161100
3.94-4.11110.075002.1871100
4.11-4.3310.90.0684812.7251100
4.33-4.610.60.0644973.0481100
4.6-4.9610.20.0644863.353199.8
4.96-5.4610.20.0644993.594199.8
5.46-6.2410.50.0565052.9731100
6.24-7.8610.30.055022.851199.6
7.86-508.40.0513993.903176.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.902→36.411 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3014 962 9.96 %
Rwork0.2558 8695 -
obs0.2603 9657 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.26 Å2 / Biso mean: 111.8936 Å2 / Biso min: 60 Å2
Refinement stepCycle: final / Resolution: 2.902→36.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 691 0 0 2503
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022614
X-RAY DIFFRACTIONf_angle_d0.4813667
X-RAY DIFFRACTIONf_chiral_restr0.029425
X-RAY DIFFRACTIONf_plane_restr0.004339
X-RAY DIFFRACTIONf_dihedral_angle_d17.8371462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9021-3.0550.42261390.33681228136798
3.055-3.24630.35311320.34681244137699
3.2463-3.49670.36811460.321912701416100
3.4967-3.84830.31821350.27941242137798
3.8483-4.40430.29731410.276912571398100
4.4043-5.54580.28621400.241912631403100
5.5458-36.41370.27111290.21131191132091

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