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- PDB-7zj1: Crystal structure of ADAR1-dsRBD3 dimer -

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Basic information

Entry
Database: PDB / ID: 7zj1
TitleCrystal structure of ADAR1-dsRBD3 dimer
ComponentsDouble-stranded RNA-specific adenosine deaminase
KeywordsRNA BINDING PROTEIN / Editing / ADAR / RNA-binding domain
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 / mRNA processing / cellular response to virus / osteoblast differentiation / protein import into nucleus / double-stranded RNA binding / Interferon alpha/beta signaling / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMboukou, A. / Barraud, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE91-0003 France
CitationJournal: Biorxiv / Year: 2023
Title: Dimerization of ADAR1 modulates site-specificity of RNA editing
Authors: Mboukou, A. / Rajendra, V. / Messmer, S. / Catala, M. / Tisne, C. / Jantsch, M.F. / Barraud, P.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Structure summary / Category: pdbx_database_related / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-specific adenosine deaminase


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.235, 44.235, 131.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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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: 9249.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR, ADAR1, DSRAD, G1P1, IFI4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P55265, double-stranded RNA adenine deaminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.01 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 100 mM sodium citrate pH 4.0, 20% (w/v) PEG 6000, and 1.0 M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.65→19.15 Å / Num. obs: 18792 / % possible obs: 99.26 % / Redundancy: 18.7 % / Biso Wilson estimate: 18.31 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1518 / Rpim(I) all: 0.03536 / Rrim(I) all: 0.156 / Net I/σ(I): 12.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible allMean I/σ(I) obs
1.65-1.70914.20.867418520.5850.8590.23810.900499.84
9.04-19.1515.10.0831380.9940.0220.08790.823

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
ARP/wARP8model building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MDR

2mdr


Resolution: 1.65→19.15 Å / SU ML: 0.1988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 943 5.05 %
Rwork0.1871 17728 -
obs0.189 18670 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.45 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 0 116 1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01031280
X-RAY DIFFRACTIONf_angle_d1.08121736
X-RAY DIFFRACTIONf_chiral_restr0.0698183
X-RAY DIFFRACTIONf_plane_restr0.01231
X-RAY DIFFRACTIONf_dihedral_angle_d14.4548455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.740.25561340.20312491X-RAY DIFFRACTION99.81
1.74-1.850.25991200.21272510X-RAY DIFFRACTION99.92
1.85-1.990.25611270.19182426X-RAY DIFFRACTION96.81
1.99-2.190.22261420.18962509X-RAY DIFFRACTION100
2.19-2.50.20341090.18882516X-RAY DIFFRACTION98.83
2.5-3.150.23111580.20162577X-RAY DIFFRACTION100
3.15-19.150.21281530.17032699X-RAY DIFFRACTION100
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)
10.456879228728-0.3224520048490.1281039191340.373197592608-0.4347896830550.8356316601810.0466221877682-0.02910892177380.0106061678279-0.021798198064-0.0873864277542-0.01936998587130.06885636629330.0892310618213-0.001418346230630.1238302732970.007531567919-0.004392739953550.121178376163-0.005103011420360.1242092561527.8894759182-9.4124802721812.9832500976
20.438596652983-0.06403628569570.1214198222660.34134123915-0.2177029155330.646016462239-0.03552919418050.0281840780872-0.0204238666584-0.07699079323620.00403438540504-0.00553917429394-0.086364645323-0.0673132453443-4.6305435798E-50.1208446479180.007032880964720.002554566287140.1296486842660.0009369359056450.12502049709413.83997378664.513728387887.5847744905
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 715 through 796)AA715 - 7961 - 82
22chain 'B' and (resid 714 through 797)BB714 - 7971 - 84

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