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- PDB-2acj: Crystal structure of the B/Z junction containing DNA bound to Z-D... -

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Basic information

Entry
Database: PDB / ID: 2acj
TitleCrystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins
Components
  • 5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*GP*GP*CP*GP*CP*GP*CP*G)-3'
  • 5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*AP*TP*AP*AP*AP*CP*C)-3'
  • Double-stranded RNA-specific adenosine deaminase
Keywordshydrolase/DNA / a B-Z juction / 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 / 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 / cellular response to virus / mRNA processing / 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 / 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 / MAD / Resolution: 2.6 Å
AuthorsHa, S.C. / Lowenhaupt, K. / Rich, A. / Kim, Y.-G. / Kim, K.K.
CitationJournal: Nature / Year: 2005
Title: Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.
Authors: Ha, S.C. / Lowenhaupt, K. / Rich, A. / Kim, Y.G. / Kim, K.K.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*AP*TP*AP*AP*AP*CP*C)-3'
F: 5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*GP*GP*CP*GP*CP*GP*CP*G)-3'
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


Theoretical massNumber of molelcules
Total (without water)39,6796
Polymers39,6796
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.765, 110.765, 61.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 5157.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic
#2: DNA chain 5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*GP*GP*CP*GP*CP*GP*CP*G)-3'


Mass: 5259.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic
#3: Protein
Double-stranded RNA-specific adenosine deaminase / DRADA / 136 kDa double-stranded RNA binding protein / P136 / K88DSRBP / Interferon-inducible ...DRADA / 136 kDa double-stranded RNA binding protein / P136 / K88DSRBP / Interferon-inducible protein 4 / IFI-4 protein


Mass: 7315.534 Da / Num. of mol.: 4 / Fragment: Zalpha domain, ADAR1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P55265, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 22-23% MPD, 55-60mM sodium acetate, 15-16mM calsium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium acetate11
3calsium chloride11
4MPD12
5sodium acetate12
6calsium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97939, 0.97952, 0.97171
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.979521
30.971711
ReflectionResolution: 2.6→50 Å / Num. obs: 13389 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rsym value: 0.046
Reflection shellResolution: 2.6→2.69 Å / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 17.072 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.049 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The structure was refined also with CNS 1.1.
RfactorNum. reflection% reflectionSelection details
Rfree0.28486 1232 9.8 %RANDOM
Rwork0.23769 ---
all0.24254 ---
obs0.24254 11327 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å21.18 Å20 Å2
2--2.37 Å20 Å2
3----3.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 691 0 0 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212691
X-RAY DIFFRACTIONr_bond_other_d0.0020.022168
X-RAY DIFFRACTIONr_angle_refined_deg1.4982.3193756
X-RAY DIFFRACTIONr_angle_other_deg0.91135164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5095242
X-RAY DIFFRACTIONr_chiral_restr0.060.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
X-RAY DIFFRACTIONr_nbd_refined0.2230.2579
X-RAY DIFFRACTIONr_nbd_other0.2240.22418
X-RAY DIFFRACTIONr_nbtor_other0.0860.21316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.210
X-RAY DIFFRACTIONr_mcbond_it1.7511.51224
X-RAY DIFFRACTIONr_mcangle_it3.421943
X-RAY DIFFRACTIONr_scbond_it2.54731467
X-RAY DIFFRACTIONr_scangle_it4.454.51813
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.509 16
Rwork0.431 797
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.60570.1437-2.63488.48171.00891.5328-0.0957-0.0352-0.39071.13390.0022-0.5428-0.09060.22790.09350.42760.0287-0.04880.21940.03030.010777.5488-6.226162.2119
22.19322.2885-0.129-0.50190.21220.51160.1613-0.24850.4431-0.1539-0.08980.2196-0.22670.0395-0.07150.22570.02390.12210.1067-0.12850.46365.969118.528843.9577
33.1340.09551.01460.8991-1.22932.48520.1171-0.0932-0.3901-0.0761-0.0780.11190.1776-0.1353-0.03910.1075-0.06450.04630.20960.0050.351254.9418-11.903440.6903
42.5687-0.34640.59382.54850.16751.72460.1246-0.3966-0.1538-0.0869-0.2262-0.08690.01080.54140.10160.0992-0.00150.0520.29320.10080.303188.5542-3.726636.772
51.6004-0.1904-1.36870.5079-0.80514.94690.0349-0.02440.29560.053-0.33620.1030.18050.12930.30120.15160.00910.05210.18870.03940.134768.86523.159837.8717
61.50240.38130.96550.4527-0.3359-3.59040.14160.01620.026-0.0027-0.0875-0.0504-0.10560.1923-0.0540.1655-0.01840.10440.17960.00560.183770.09190.461330.5054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC-2 - 1992 - 63
2X-RAY DIFFRACTION2BD-2 - 2022 - 66
3X-RAY DIFFRACTION3CE-3 - 2001 - 64
4X-RAY DIFFRACTION4DF-3 - 1991 - 63
5X-RAY DIFFRACTION5EA1 - 171 - 17
6X-RAY DIFFRACTION6FB18 - 341 - 17

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