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- PDB-7c0j: Crystal structure of chimeric mutant of GH5 in complex with Z-DNA -

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Basic information

Entry
Database: PDB / ID: 7c0j
TitleCrystal structure of chimeric mutant of GH5 in complex with Z-DNA
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
  • Histone H5,Double-stranded RNA-specific adenosine deaminase
KeywordsDNA BINDING PROTEIN/DNA / GH5 / Protein-DNA complex / protein engineering / Z-DNA binding protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / negative regulation of DNA recombination / RISC complex assembly / pre-miRNA processing / definitive hemopoiesis / chromosome condensation / negative regulation of type I interferon-mediated signaling pathway / nucleosomal DNA binding / hepatocyte apoptotic process / RNA processing / positive regulation of viral genome replication / hematopoietic progenitor cell differentiation / protein export from nucleus / erythrocyte differentiation / PKR-mediated signaling / cellular response to virus / response to virus / mRNA processing / protein import into nucleus / osteoblast differentiation / structural constituent of chromatin / Interferon alpha/beta signaling / nucleosome / nucleosome assembly / double-stranded RNA binding / chromatin organization / double-stranded DNA 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) / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / Histone H5 / Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsChoi, H.J. / Park, C.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063903 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process.
Authors: Park, C. / Zheng, X. / Park, C.Y. / Kim, J. / Lee, S.K. / Won, H. / Choi, J. / Kim, Y.G. / Choi, H.J.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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: Histone H5,Double-stranded RNA-specific adenosine deaminase
B: Histone H5,Double-stranded RNA-specific adenosine deaminase
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,4474
Polymers20,4474
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-21 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.135, 47.305, 57.118
Angle α, β, γ (deg.)90.000, 98.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone H5,Double-stranded RNA-specific adenosine deaminase


Mass: 8109.267 Da / Num. of mol.: 2 / Mutation: K41G,S42E,R43G,K53A,R95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human)
Gene: ADAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02259, UniProt: P55265
#2: DNA chain DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Mass: 2114.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES pH 6.0, PEG 4000, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 4625 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Χ2: 0.993 / Net I/σ(I): 7.4 / Num. measured all: 16934
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.50.5922350.8220.3640.6970.965100
2.75-2.83.60.4492310.8540.2740.5270.85999.6
2.8-2.853.60.3832410.9050.2330.4490.896100
2.85-2.913.70.3292100.9010.1990.3850.943100
2.91-2.973.80.262340.9230.1540.3020.864100
2.97-3.043.70.222190.9770.1320.2570.852100
3.04-3.123.80.1912440.9810.1140.2220.893100
3.12-3.23.70.1872220.980.1120.2181.006100
3.2-3.33.70.1462210.9890.0870.170.797100
3.3-3.43.70.1262390.990.0750.1470.914100
3.4-3.523.70.0982330.9890.0580.1140.905100
3.52-3.663.70.0932230.990.0550.1081.087100
3.66-3.833.70.0762320.9970.0460.0891.156100
3.83-4.033.70.0792320.9880.0480.0931.095100
4.03-4.293.70.0772270.9870.0460.091.2100
4.29-4.623.60.0672340.9890.0410.0791.181100
4.62-5.083.60.062330.9910.0370.072.42999.6
5.08-5.813.40.0472330.9970.0290.0550.627100
5.81-7.323.70.0442350.9960.0270.0520.593100
7.32-503.50.0252470.9980.0160.030.59298

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000720data reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000720data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HST

1hst


Resolution: 2.75→28.876 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 210 4.99 %
Rwork0.2229 3996 -
obs0.2243 4206 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.32 Å2 / Biso mean: 42.9232 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 2.75→28.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 246 0 10 1179
Biso mean---27.34 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7502-3.46410.2834970.2609190993
3.4641-28.8760.23081130.20562087100
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)
14.12351.10572.725.6994-1.39473.142-0.1009-0.4007-0.39341.23370.1787-0.49380.67130.1955-0.08630.69960.153-0.08350.2426-0.06180.32916.2148-11.513542.7142
22.6422-2.65621.34937.3492-1.0196.59120.1124-0.1464-0.1626-0.29920.31570.3779-0.3723-0.2181-0.31260.1559-0.04370.03290.17010.05990.3093-14.4156-12.743912.7669
34.18272.65331.59212.2406-0.17335.78180.02590.09730.1057-0.0830.2955-0.97690.29040.2088-0.25080.15660.00530.02230.2062-0.0150.3079-0.7274-11.761429.2848
45.544-1.87681.81682.11162.25636.18010.02890.12910.04370.03310.09590.0348-0.1299-0.32280.00020.2812-0.01190.09650.1406-0.00330.3021-3.9719-12.741724.2563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 27 through 97)A27 - 97
2X-RAY DIFFRACTION2(chain 'B' and resid 27 through 97)B27 - 97
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 6)D1 - 6
4X-RAY DIFFRACTION4(chain 'E' and resid 1 through 6)E1 - 6

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