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- PDB-7zlq: Crystal structure of ADAR1-dsRBD3 dimer in complex with dsRNA -

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Basic information

Entry
Database: PDB / ID: 7zlq
TitleCrystal structure of ADAR1-dsRBD3 dimer in complex with dsRNA
Components
  • Double-stranded RNA-specific adenosine deaminase
  • RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')
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 / 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 / RNA processing / hematopoietic progenitor cell differentiation / 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 / cytoplasm / cytosol
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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMboukou, A. / Barraud, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE91-0003 France
CitationJournal: Nat Commun / Year: 2024
Title: Dimerization of ADAR1 modulates site-specificity of RNA editing
Authors: Mboukou, A. / Rajendra, V. / Messmer, S. / Mandl, T.C. / Catala, M. / Tisne, C. / Jantsch, M.F. / Barraud, P.
History
DepositionApr 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-specific adenosine deaminase
C: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')
D: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')
E: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)30,8965
Polymers30,8965
Non-polymers00
Water00
1
A: Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-specific adenosine deaminase
C: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')
D: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')
E: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')

C: RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)35,0296
Polymers35,0296
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)91.294, 91.294, 207.527
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2chain "A"
d_2ens_2chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAASNA1 - 82
d_21ens_1ALAASNB1 - 82
d_11ens_2ALAASNA1 - 82
d_21ens_2ALAASNB1 - 82

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.997808792496, 0.000786642855295, -0.0661588604074), (-0.00101045884781, -0.999993879509, 0.00334961456074), (-0.0661558205323, 0.00340912566604, 0.997803480287)-2.78578893056, -54.8367713548, -0.0330357189179
2given(-0.997808792496, 0.000786642855295, -0.0661588604074), (-0.00101045884781, -0.999993879509, 0.00334961456074), (-0.0661558205323, 0.00340912566604, 0.997803480287)-2.78578893056, -54.8367713548, -0.0330357189179

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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: RNA chain RNA (5'-R(*CP*GP*AP*AP*GP*CP*CP*UP*UP*CP*GP*CP*G)-3')


Mass: 4132.518 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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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: 4.04 Å3/Da / Density % sol: 69.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM sodium cacodylate, 5% (w/v) PEG 4000, 30 mM CaCl2, 230 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.8→44.58 Å / Num. obs: 10044 / % possible obs: 94.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 37.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.038 / Rrim(I) all: 0.167 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.9918.32.6631.25030.5170.6332.73988.6
8.89-44.5816.10.03161.850210.010.032100

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
PHASER2.8.2phasing
REFMAC5.8.0refinement
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZJ1

7zj1


Resolution: 2.8→44.58 Å / SU ML: 0.2653 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.3849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1078 10.75 %
Rwork0.231 8949 -
obs0.2349 10027 75.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 819 0 0 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672204
X-RAY DIFFRACTIONf_angle_d0.87813162
X-RAY DIFFRACTIONf_chiral_restr0.0548372
X-RAY DIFFRACTIONf_plane_restr0.0095271
X-RAY DIFFRACTIONf_dihedral_angle_d12.7053926
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.546201441953
ens_2d_2AX-RAY DIFFRACTIONTorsion NCS0.546201441953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.3421390.3404255X-RAY DIFFRACTION18.22
2.93-3.090.3006690.2579463X-RAY DIFFRACTION33.46
3.09-3.280.2147870.208745X-RAY DIFFRACTION51.61
3.28-3.530.27041540.24651434X-RAY DIFFRACTION97.78
3.53-3.890.22661780.21891449X-RAY DIFFRACTION99.75
3.89-4.450.25621700.22681478X-RAY DIFFRACTION99.88
4.45-5.610.2441910.22921492X-RAY DIFFRACTION99.88
5.61-44.580.31591900.23141633X-RAY DIFFRACTION99.89
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)
14.21988058034-1.24757360106-0.6981694001645.908066522910.3889367357941.160517011520.2694483890070.759296905594-0.759311308692-1.3560970318-0.3002083018140.3718005309560.464885015711-0.02072193657660.007177938420391.319529519430.450325521957-0.2322285983590.494258871238-0.05427309903040.683462081913-0.0231507173332-37.8134557175-2.68944067811
22.167225151150.02717414747660.3993722846372.01372739371-1.399188618763.466801082610.214460281710.585502534424-0.0733545159247-0.818542198532-0.233066150284-0.133904439430.2307289782290.526377420890.07292312985791.170587785350.335946457986-0.0311882272140.464693670530.0836076255480.244056044017-2.61410113494-17.032502407-2.84491484678
30.6453266200190.3143034541470.1660714408350.2916493822790.3266716938420.726501359656-0.05784178411830.1588659855270.0800394143831-0.0715148591850.177048516090.1329897141930.05273348513420.06935272766320.07718809673670.8252838227940.133910510990.07488742183640.477896416330.3079183958180.174119672763-13.3171993643-1.688717930034.27162643195
45.567295554291.394973003512.987923176840.9126941141480.2138408127563.997167053060.001070941591340.683208423686-0.184815728862-0.5701518578270.262287314211-0.0739502284269-0.191923579062-0.391247154284-0.1673975603111.454006924130.492397865319-0.2537225661420.790198669342-0.09210541742330.6453287377029.96026286452-53.39982669434.87948397947
52.873227907592.142506016132.764092988872.207651373932.338500618922.78507605790.0273727525640.894987347994-0.06746372733-0.5845154978420.1378433643150.03807432890280.2900490111150.14845195994-0.1238914544391.593274348760.426556482859-0.2668907646780.999552696337-0.2704306935050.67429188620910.9731207946-56.0604420426-3.94646488411
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 715 through 796)AA715 - 7961 - 82
22(chain 'B' and resid 715 through 796)BB715 - 7961 - 82
33(chain 'C' and resid 1 through 13)CC1 - 13
44(chain 'D' and resid 1 through 13)DD1 - 13
55(chain 'E' and resid 1 through 13)EE1 - 13

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