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- PDB-5zu1: Crystal Structure of BZ junction in diverse sequence -

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Basic information

Entry
Database: PDB / ID: 5zu1
TitleCrystal Structure of BZ junction in diverse sequence
Components
  • DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*AP*GP*GP*CP*GP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*TP*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 / supraspliceosomal complex / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / adenosine to inosine editing / negative regulation of protein kinase activity by regulation of protein phosphorylation / double-stranded RNA adenosine deaminase activity ...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 / supraspliceosomal complex / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / adenosine to inosine editing / negative regulation of protein kinase activity by regulation of protein phosphorylation / double-stranded RNA adenosine deaminase activity / base conversion or substitution editing / response to interferon-alpha / hematopoietic stem cell homeostasis / negative regulation of hepatocyte apoptotic process / RISC complex assembly / pre-miRNA processing / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / RNA processing / hematopoietic progenitor cell differentiation / positive regulation of viral genome replication / protein export from nucleus / erythrocyte differentiation / PKR-mediated signaling / cellular response to virus / response to virus / mRNA processing / protein import into nucleus / osteoblast differentiation / Interferon alpha/beta signaling / double-stranded RNA binding / defense response to virus / innate immune response / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / 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. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) ...ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / 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 / MOLECULAR REPLACEMENT / Resolution: 3.009 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 5, 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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*CP*TP*TP*AP*AP*AP*CP*C)-3')
F: DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*AP*GP*GP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)38,2456
Polymers38,2456
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-48 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.920, 108.920, 62.004
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: 6957.144 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*CP*TP*TP*AP*AP*AP*CP*C)-3')


Mass: 5148.337 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*AP*GP*GP*CP*GP*CP*GP*CP*G)-3')


Mass: 5268.409 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: 55.69 % / Mosaicity: 0.482 °
Crystal growTemperature: 296 K / Method: batch mode / pH: 4.5
Details: 25% 2-methyl-2,4-pentanediol (MPD), 100mM NaOAC, pH 4.5

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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: 3→20 Å / Num. obs: 8369 / % possible obs: 99.5 % / Redundancy: 10.5 % / Biso Wilson estimate: 97.03 Å2 / Rmerge(I) obs: 0.059 / Χ2: 2.455 / Net I/σ(I): 21.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.1111.20.3998391.0511100
3.11-3.2311.30.2588231.2931100
3.23-3.3811.30.1758401.691100
3.38-3.5511.20.138302.0591100
3.55-3.787.80.1018332.9321100
3.78-4.0610.60.0868353.0651100
4.06-4.4710.50.0668523.381100
4.47-5.1110.40.0588393.5161100
5.11-6.410.50.0498473.231199.9
6.4-209.60.0358312.765195.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACJ

2acj


Resolution: 3.009→19.994 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.38
RfactorNum. reflection% reflection
Rfree0.2797 836 10.04 %
Rwork0.2332 --
obs0.2378 8328 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.54 Å2 / Biso mean: 98.9135 Å2 / Biso min: 50.76 Å2
Refinement stepCycle: final / Resolution: 3.009→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 631 0 0 2372
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112475
X-RAY DIFFRACTIONf_angle_d1.693458
X-RAY DIFFRACTIONf_chiral_restr0.111393
X-RAY DIFFRACTIONf_plane_restr0.009324
X-RAY DIFFRACTIONf_dihedral_angle_d24.159975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0089-3.19680.37051340.31811221135598
3.1968-3.44240.38431380.275612501388100
3.4424-3.78670.31761410.26961244138599
3.7867-4.32980.28531380.24312671405100
4.3298-5.43690.2921430.227612581401100
5.4369-19.99440.22671420.20081252139497

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