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- PDB-8e4x: Human Adenosine Deaminase Acting on dsRNA (ADAR2-R2D) bound to ds... -

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Basic information

Entry
Database: PDB / ID: 8e4x
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2-R2D) bound to dsRNA containing a G:3-deaza dA pair adjacent to the target site
Components
  • Double-stranded RNA-specific editase 1
  • RNA (5-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*GP*(8AZ)P*GP*AP*GP*GP*GP*CP* UP*CP*UP*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)
  • RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*(4DU)*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)
KeywordsRNA binding protein/RNA / Protein-RNA complex / RNA editing / RNA binding protein / RNA binding protein-RNA complex
Function / homology
Function and homology information


hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation ...hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / neuromuscular process controlling posture / adenosine to inosine editing / neuromuscular synaptic transmission / innervation / motor behavior / motor neuron apoptotic process / positive regulation of viral genome replication / RNA processing / negative regulation of cell migration / multicellular organism growth / mRNA processing / double-stranded RNA binding / defense response to virus / regulation of cell cycle / negative regulation of cell population proliferation / innate immune response / mRNA binding / synapse / nucleolus / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ADAR2, first double-stranded RNA binding domain / ADAR2, second double-stranded RNA binding domain / 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 / Cytokine IL1/FGF / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFisher, A.J. / Mendoza, H.G.
Funding support Netherlands, United States, 3items
OrganizationGrant numberCountry
Other privateProQR Therapeutics PT20BPA Netherlands
Other privateRett Syndrome Research Trust RT19PB United States
Other governmentCRCCFAJ United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site.
Authors: Doherty, E.E. / Karki, A. / Wilcox, X.E. / Mendoza, H.G. / Manjunath, A. / Matos, V.J. / Fisher, A.J. / Beal, P.A.
History
DepositionAug 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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-specific editase 1
B: Double-stranded RNA-specific editase 1
C: RNA (5-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*GP*(8AZ)P*GP*AP*GP*GP*GP*CP* UP*CP*UP*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)
D: RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*(4DU)*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9828
Polymers128,5314
Non-polymers1,4514
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-157 kcal/mol
Surface area43110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.914, 63.236, 142.646
Angle α, β, γ (deg.)90.000, 118.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Double-stranded RNA-specific editase 1 / RNA-editing deaminase 1 / RNA-editing enzyme 1 / dsRNA adenosine deaminase


Mass: 53989.715 Da / Num. of mol.: 2 / Mutation: E488Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADARB1, ADAR2, DRADA2, RED1 / Plasmid: pSc ADAR / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123
References: UniProt: P78563, double-stranded RNA adenine deaminase

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RNA chain , 2 types, 2 molecules CD

#2: RNA chain RNA (5-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*GP*(8AZ)P*GP*AP*GP*GP*GP*CP* UP*CP*UP*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)


Mass: 10355.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: generated by solid phase oligonucleotide synthesis / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*(4DU)*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)


Mass: 10196.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: generated by solid phase oligonucleotide synthesis / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 42 molecules

#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 50 mM MOPS pH 7.0, 100 mM NaCl, 13% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→58.27 Å / Num. obs: 31664 / % possible obs: 95.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 84.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12 / Num. measured all: 99409 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.8-2.951.1751500947410.5241.298.1
8.85-58.270.02230039470.99946.686.1

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Processing

Software
NameVersionClassification
Aimless0.7.9data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.18phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vff

6vff


Resolution: 2.8→58.27 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1578 4.99 %
Rwork0.195 30068 -
obs0.1973 31646 94.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.24 Å2 / Biso mean: 110.7111 Å2 / Biso min: 67.36 Å2
Refinement stepCycle: final / Resolution: 2.8→58.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 1359 74 38 8029
Biso mean--83.73 93.8 -
Num. residues----902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.890.44441480.38252832298098
2.89-2.990.39841440.35162770291498
2.99-3.110.35481370.30612819295698
3.11-3.260.30541490.25592689283895
3.26-3.430.28271260.22542729285595
3.43-3.640.26641480.21482804295297
3.64-3.920.2231480.18912755290397
3.92-4.320.26671340.17562766290096
4.32-4.940.22431500.16162593274390
4.94-6.220.20981490.18382688283793
6.23-58.270.18421450.15562623276888
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)
11.65430.30890.69341.5270.21831.10130.08730.10680.0272-0.09190.0061-0.1203-0.0170.12270.00020.68520.01580.09740.8031-0.04760.7057-28.92815.78928.291
20.3020.13040.00340.46240.45550.31720.1869-0.09770.32760.2904-0.30030.4521-0.3627-0.4457-0.00560.8249-0.06820.05330.77560.03780.8344-45.11826.41544.873
31.977-0.50750.13611.65770.2091.40880.06680.06280.05940.23360.0798-0.2611-0.02660.09310.00010.79730.0292-0.01530.7775-0.01330.8097-34.56117.74435.382
40.63510.2696-0.1552-0.02720.56930.61790.09750.006-0.23010.34020.0081-0.04430.1340.06890.00011.07540.0204-0.10780.73640.00530.9134-41.1633.35237.238
50.381-0.1722-0.3640.4528-0.0240.2623-0.58130.17390.0270.01120.4706-0.0749-0.1451-0.5341-0.00041.4154-0.0807-0.14281.40480.05630.8823-73.52523.5715.397
60.523-0.09910.01381.17420.05980.52750.10020.2144-0.11670.05950.03290.1335-0.1504-0.08840.00040.750.00210.01980.98140.02220.961-83.44316.75740.824
70.31410.0762-0.08690.01450.00340.0415-0.1878-0.15920.37810.1735-0.40150.2032-0.1481-0.3587-0.00260.7299-0.08220.0070.8470.06651.0763-62.3268.84545.404
82.1501-0.3608-0.39382.0207-0.36850.896-0.0414-0.0031-0.21520.36040.03070.0444-0.1232-0.1084-0.00010.8232-0.02620.00980.8461-0.01450.9137-75.511.94146.639
90.6019-0.06530.68130.6972-0.25460.5662-0.3875-0.3694-0.85190.07370.04940.42470.01910.11060.00031.1360.02990.15411.00950.04491.174-83.2344.47658.481
100.4476-0.568-0.44441.0469-0.01430.48160.27550.00970.0294-0.40210.0504-0.1818-0.7948-0.4051-0.00020.94270.034-0.0710.99410.0270.9496-46.38539.38541.553
110.19360.43770.28450.4375-0.72320.62480.10050.5872-0.05070.3470.59230.2249-0.4031-1.19180.00121.41730.2013-0.00031.80320.09011.0323-59.65131.442-0.415
12-0.10720.513-0.22590.3284-0.75240.7029-0.03650.1014-0.1706-0.48830.259-0.4403-2.74-1.26090.00131.84030.04250.01771.55310.07411.2251-56.21133.6585.117
130.2017-0.1083-0.8424-0.05240.29630.77240.0047-0.2518-0.2425-0.54520.1924-0.259-1.3821-0.206-0.00061.1020.093-0.0520.9806-0.03561.0094-45.342.40148.657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 316:473 )A316 - 473
2X-RAY DIFFRACTION2( CHAIN A AND RESID 474:499 )A474 - 499
3X-RAY DIFFRACTION3( CHAIN A AND RESID 500:617 )A500 - 617
4X-RAY DIFFRACTION4( CHAIN A AND RESID 618:699 )A618 - 699
5X-RAY DIFFRACTION5( CHAIN B AND RESID 235:310 )B235 - 310
6X-RAY DIFFRACTION6( CHAIN B AND RESID 311:463 )B311 - 463
7X-RAY DIFFRACTION7( CHAIN B AND RESID 476:488 )B476 - 488
8X-RAY DIFFRACTION8( CHAIN B AND RESID 489:637 )B489 - 637
9X-RAY DIFFRACTION9( CHAIN B AND RESID 638:700 )B638 - 700
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:17 )C1 - 17
11X-RAY DIFFRACTION11( CHAIN C AND RESID 18:32 )C18 - 32
12X-RAY DIFFRACTION12( CHAIN D AND RESID 1:17 )D1 - 17
13X-RAY DIFFRACTION13( CHAIN D AND RESID 18:32 )D18 - 32

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