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- PDB-1qbj: CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qbj
TitleCRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
  • PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))
KeywordsHYDROLASE/DNA / PROTEIN-Z-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 / hematopoietic progenitor cell differentiation / RNA processing / 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 / 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. / 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 / Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsSchwartz, T. / Rould, M.A. / Rich, A.
CitationJournal: Science / Year: 1999
Title: Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA.
Authors: Schwartz, T. / Rould, M.A. / Lowenhaupt, K. / Herbert, A. / Rich, A.
History
DepositionApr 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 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
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
A: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))
B: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))
C: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))


Theoretical massNumber of molelcules
Total (without water)33,3506
Polymers33,3506
Non-polymers00
Water4,396244
1
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
A: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))
B: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))


Theoretical massNumber of molelcules
Total (without water)22,2334
Polymers22,2334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
C: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))

F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
C: PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))


Theoretical massNumber of molelcules
Total (without water)22,2334
Polymers22,2334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)85.900, 85.900, 71.300
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-237-

HOH

21C-514-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.990644, 0.072102, -0.115866), (0.073321, -0.997289, 0.006288), (-0.115098, -0.014724, -0.993245)0.60064, 25.44796, 25.25727
2given(-0.710719, 0.701864, 0.047593), (-0.702308, -0.71181, 0.009454), (0.040513, -0.026705, 0.998822)11.74451, 30.69955, 23.68195
3given(-0.658349, -0.752328, 0.024065), (-0.748761, 0.65783, 0.081342), (-0.077026, 0.035533, -0.996396)30.65003, 12.33563, 47.9721
4given(0.994153, 0.067559, -0.084235), (0.066323, -0.997647, -0.017391), (-0.085212, 0.011702, -0.996294)0.12342, 25.8724, 24.33724
5given(-0.715126, 0.694991, 0.074715), (-0.697008, -0.717062, -0.001298), (0.052673, -0.053005, 0.997204)11.49656, 30.82336, 23.98233
6given(-0.668698, -0.743519, -0.004831), (-0.742703, 0.667629, 0.051608), (-0.035146, 0.038098, -0.998656)30.89219, 12.37642, 47.28941

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Components

#1: DNA chain DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Mass: 2114.398 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: SYNTHETIC
#2: Protein PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))


Mass: 9002.293 Da / Num. of mol.: 3 / Fragment: N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): NOVABLUE (DE3) / References: UniProt: P55265
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.97 Å3/Da / Density % sol: 37 %
Crystal growpH: 5.6
Details: HANGING DROP VAPOR DIFFUSION OVER 1.6 M (NH4)2SO4, 10 % GLYCEROL AT 24 DEGREES CELSIUS, pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
210 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 29702 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rsym value: 0.074 / Net I/σ(I): 27.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.535 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.535

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1521 10 %RANDOM
Rwork0.227 ---
obs0.227 13519 99.8 %-
Displacement parametersBiso mean: 29.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 369 0 244 2142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.04
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.08
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3315 147 8.5 %
Rwork0.3892 1575 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARNDBX.DNATOPNDBX.DNA
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08

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