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- PDB-7c0i: Crystal structure of chimeric mutant of E3L in complex with Z-DNA -

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Basic information

Entry
Database: PDB / ID: 7c0i
TitleCrystal structure of chimeric mutant of E3L in complex with Z-DNA
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
  • Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
KeywordsDNA BINDING PROTEIN / E3L / Protein-DNA complex / protein engineering / Z-DNA binding protein
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / suppression by virus of host type I interferon production / adenosine to inosine editing / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / RISC complex assembly / evasion of host immune response / negative regulation of hepatocyte apoptotic process / pre-miRNA processing / protein serine/threonine kinase inhibitor activity / 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 sequestering activity / 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 / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / defense response to virus / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / innate immune response / virus-mediated perturbation of host defense response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Protein E3 / 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 ...Protein E3 / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / RNA-binding protein OPG065 / Double-stranded RNA-specific adenosine deaminase / Double-stranded RNA-binding protein
Similarity search - Component
Biological speciesVaccinia virus
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsChoi, H.J. / Park, C.H. / Kim, J.S.
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 2.0Nov 2, 2022Group: Database references / Polymer sequence / Structure summary
Category: database_2 / entity / entity_poly
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.type
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
C: Double-stranded RNA-binding protein,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')
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8817
Polymers33,7856
Non-polymers961
Water55831
1
A: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-binding protein,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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6195
Polymers22,5234
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-35 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)22,5234
Polymers22,5234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area3110 Å2
ΔGint-22 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.759, 72.759, 123.876
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase


Mass: 9147.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus, (gene. exp.) Homo sapiens (human)
Gene: E3L, ADAR1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86638, UniProt: P55265, UniProt: P21605*PLUS
#2: 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 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Sodium citrate pH 4.0, Ammonium sulfate, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14894 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.026 / Rrim(I) all: 0.055 / Χ2: 0.949 / Net I/σ(I): 9.9 / Num. measured all: 66340
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.40.4697290.8620.2470.5310.45198.1
2.44-2.494.70.3837440.9090.1940.430.43499.1
2.49-2.534.60.3427140.9340.1760.3850.45999.3
2.53-2.594.60.2777400.9540.1440.3140.4699.3
2.59-2.644.50.2397310.9630.1250.270.48799.2
2.64-2.74.50.1977420.9710.1030.2230.50799.5
2.7-2.774.30.1467320.9810.0790.1660.55899.5
2.77-2.854.20.1137350.9860.0620.130.61999.3
2.85-2.934.60.0967540.9890.050.1080.66899.6
2.93-3.024.60.0877350.9910.0450.0990.75199.3
3.02-3.134.60.0737310.9930.0380.0830.87399.6
3.13-3.264.50.0677430.9930.0350.0760.99299.6
3.26-3.414.30.0657480.9920.0350.0741.24199.6
3.41-3.584.30.0577410.9940.0310.0651.44299.6
3.58-3.814.70.0567540.9950.0280.0631.53499.7
3.81-4.14.50.0517530.9950.0270.0581.52199.7
4.1-4.524.30.0457500.9970.0240.0521.52299.6
4.52-5.174.50.0457580.9970.0240.0511.48799.6
5.17-6.514.40.0447640.9970.0230.051.36799.9
6.51-504.10.0377960.9970.0210.0431.63898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1qbj


Resolution: 2.4→34.905 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 759 5.1 %
Rwork0.2016 14118 -
obs0.2028 14877 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.24 Å2 / Biso mean: 92.0576 Å2 / Biso min: 46.65 Å2
Refinement stepCycle: final / Resolution: 2.4→34.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 389 5 31 1952
Biso mean--157.07 67.65 -
Num. residues----212
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.58540.3811900.2975273699
2.5854-2.84550.29371260.2774281699
2.8455-3.2570.27451500.2482809100
3.257-4.10240.22451490.20212845100
4.1024-34.9050.19131440.1742912100
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)
17.13770.79833.75620.48-0.71165.32111.2340.9258-2.5329-2.1018-0.92020.83592.3995-0.5737-2.04341.28970.1429-0.48461.3618-0.75831.5796-23.98-24.621-31.97
25.1741-3.48862.29442.7381-1.0893.45420.91910.3355-2.9413-0.79690.27070.5722-0.0095-1.9067-0.8210.7714-0.1868-0.23841.3671-0.21721.5014-30.772-20.953-25.582
39.028-3.5402-6.30218.87912.31174.4365-0.37571.2936-0.6094-0.1653-0.30850.45240.8002-0.19060.49650.45230.0375-0.06030.9525-0.21060.6846-19.657-15.156-26.551
42.88890.7424-2.97594.52812.00614.83471.60693.0507-1.3874-2.6389-1.55370.83291.25491.0520.08751.26220.405-0.27762.0611-0.65550.9928-14.599-19.879-35.151
56.59081.5059-3.44247.3003-0.54054.06660.15680.29450.15460.2589-0.59030.0111-0.3578-0.29720.42710.68190.0233-0.13570.6912-0.12160.5376-23.4177.1174.772
64.4016-4.3734-2.10414.53772.77932.944-0.24290.7980.51260.1792-0.48130.0352-1.1137-1.59570.67380.90360.2286-0.15230.9954-0.19330.7796-29.5147.33-13.255
75.1282-5.1095-5.6945.04595.66496.33510.8017-0.01371.2696-0.8250.7084-0.8837-1.8592-0.2332-1.29931.1341-0.119-0.06820.81870.13080.8202-22.06213.288-17.454
83.57555.4074-1.45668.1868-2.57156.42760.49130.23131.07921.1707-0.14090.2229-1.4566-1.7884-0.3680.96740.2734-0.14731.0239-0.1890.7285-31.1967.201-3.165
98.511-2.40442.14572.68381.74463.1542-0.42510.22480.85350.13920.2796-0.5645-0.66480.87050.3710.7955-0.2251-0.08760.7761-0.0880.8564-18.1959.507-5.851
103.4737-2.989-2.51524.2682-0.6156.33850.2350.2702-0.07490.2286-0.05560.50490.2181-0.6311-0.18180.5908-0.1277-0.01730.5763-0.13490.555-18.0278.80213.115
112.6267-1.6362-4.47715.95921.6389.5562-0.27741.1786-0.0218-0.6101-0.16090.2255-0.8179-0.32370.26740.4243-0.0306-0.04410.9004-0.15680.5332-23.707-6.087-23.926
125.5435-3.7738-4.19358.1875-2.14818.3939-0.64791.093-0.4125-0.55660.6190.7734-0.1811-0.4340.04380.5122-0.084-0.09530.9702-0.13110.547-24.966-0.888-20.234
136.99425.51575.51699.38684.52664.26190.1158-0.8807-0.60450.592-0.0151-1.0285-0.06230.0801-0.24190.6862-0.0879-0.04510.6043-0.1280.7071-8.6093.98318.49
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:28 )A9 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:39 )A29 - 39
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1169:1182 )A1169 - 1182
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1183:1184 OR 56:70 )A1183 - 70
5X-RAY DIFFRACTION5( CHAIN B AND RESID 3:39 )B3 - 39
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1169:1184 OR 56:58 )B1169 - 58
7X-RAY DIFFRACTION7( CHAIN B AND RESID 59:69 )B59 - 69
8X-RAY DIFFRACTION8( CHAIN C AND RESID 6:19 )C6 - 19
9X-RAY DIFFRACTION9( CHAIN C AND RESID 20:39 )C20 - 39
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1169:1184 OR 56:70 )C1169 - 70
11X-RAY DIFFRACTION11( CHAIN D AND RESID 1:6 )D1 - 6
12X-RAY DIFFRACTION12( CHAIN E AND RESID 1:6 )E1 - 6
13X-RAY DIFFRACTION13( CHAIN F AND RESID 0:6 )F0 - 6

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