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- PDB-8e0f: Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsR... -

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Basic information

Entry
Database: PDB / ID: 8e0f
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing a G-G 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*GP*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: 2.7 Å
AuthorsWilcox, X.E. / Fisher, A.J. / Beal, P.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Other privateProQR Therapeutics PT20BPA
Other privateRett syndrome Research Trust RET19PB
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 9, 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*GP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0158
Polymers128,5644
Non-polymers1,4514
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-154 kcal/mol
Surface area43150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.518, 63.389, 142.135
Angle α, β, γ (deg.)90.000, 117.690, 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 / Fragment: ADAR2-R2D / 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*GP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)


Mass: 10229.155 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, 45 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.: 41 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 50 mM MOPS pH 7.0, 17% (w/v) PEG 4000, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→125.85 Å / Num. obs: 36652 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 70.39 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.051 / Rrim(I) all: 0.091 / Net I/σ(I): 9.6 / Num. measured all: 112747 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.8230.72844670.6160.50.88898.6
9.35-125.853.10.0399100.9950.0260.04794.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless2.7.28data scaling
PHENIX1.18phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VFF

6vff


Resolution: 2.7→65.73 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 3358 5.07 %
Rwork0.1933 62871 -
obs0.1952 36652 90.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.72 Å2 / Biso mean: 88.2612 Å2 / Biso min: 43.05 Å2
Refinement stepCycle: final / Resolution: 2.7→65.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 1361 74 41 8034
Biso mean--63.28 67.14 -
Num. residues----902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.740.42071780.34642691286994
2.74-2.780.39021570.34512690284793
2.78-2.820.37711380.32242603274192
2.82-2.870.36981510.30132599275090
2.87-2.920.32461220.28262517263987
2.92-2.970.3211530.29342734288795
2.97-3.030.32761270.28472746287394
3.03-3.090.2981200.28242730285095
3.09-3.160.33361620.27592778294095
3.16-3.230.31461190.26462690280994
3.23-3.310.30731310.24162733286494
3.31-3.40.26421350.22542657279293
3.4-3.50.25211540.20872701285592
3.5-3.610.21981260.20862580270691
3.61-3.740.23481500.20752649279991
3.74-3.890.22881240.20942590271490
3.89-4.070.19141420.17262520266288
4.07-4.290.25281090.16222419252883
4.29-4.550.23321460.14342586273289
4.55-4.910.15361550.14362526268190
4.91-5.40.18191510.15872595274690
5.4-6.180.23681460.1662555270189
6.18-7.780.17511370.17582505264287
7.79-65.730.17581250.14122477260286
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)
12.11170.2294-0.06191.99890.08541.34840.01130.20140.0433-0.17830.117-0.45430.02080.35670.00040.63660.04170.05390.7381-0.0630.6744-28.85915.80828.102
20.845-0.0349-0.05890.88020.89880.70660.0445-0.5670.10210.2305-0.15110.3222-0.1583-0.6896-0.0040.6915-0.029500.66640.03450.6179-44.88826.42144.781
32.3611-0.05240.26052.26450.46651.37060.00170.12030.03410.08770.0602-0.3304-0.06720.19790.00030.57280.0328-0.00940.58670.0010.5368-34.37617.75835.402
41.29970.15531.26292.73771.15721.79990.19610.0654-0.32070.1812-0.04750.12310.32760.0797-0.00020.7158-0.0301-0.04490.58080.02060.6455-41.0133.33337.202
50.6550.0153-0.62450.9643-0.34050.714-0.37340.50140.3191-0.45550.3490.3291-0.0208-0.9772-0.00181.2813-0.1058-0.1871.53970.07221.02-73.41423.6415.495
63.8604-0.0246-1.11891.6559-0.31.89250.00120.3823-0.12980.02570.09960.3339-0.1135-0.3179-0.0010.6515-0.0023-0.00990.75050.04910.7831-83.20216.81440.967
70.6258-0.00940.11470.3282-0.40290.633-0.3369-0.0474-0.4672-0.28120.2623-0.3458-0.57210.40080.0010.7174-0.07150.00250.76310.08830.9682-61.9128.8545.657
83.3565-0.1508-1.343.7684-0.13211.8038-0.0614-0.1046-0.22820.3210.11620.03360.08110.0140.00080.6096-0.01590.02160.68220.02160.7006-75.26112.18146.86
91.38980.3692-0.26571.7025-0.37822.1793-0.4063-0.6467-0.53180.5890.19110.45240.15240.0783-0.00070.95390.02380.21880.84580.11340.9578-82.94.6958.683
100.0169-0.0054-0.35621.64550.59050.74260.1046-0.0487-0.1521-0.34160.1731-0.0953-0.6214-0.222100.78290.0089-0.08110.83680.03510.7055-46.09339.39541.578
110.0233-0.05340.2735-0.0351-0.3530.5397-0.10011.0349-0.5250.29010.4103-0.02560.54940.5537-0.00081.547-0.11-0.00761.92070.12871.0712-60.10631.221-0.22
120.0636-0.12520.22540.3381-0.79760.75860.01690.2397-0.04290.30280.0885-0.2976-1.3082-0.3267-0.00131.6969-0.1028-0.14161.59960.1451.1746-56.65933.5965.23
131.04940.0244-1.05561.8163-0.7661.23640.034-0.3061-0.1228-0.39740.1667-0.0458-1.0814-0.3152-00.89780.0934-0.00530.7202-0.0330.6646-44.99142.35248.618
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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