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- PDB-9op3: Structure of Human ADAR2-R2D complexed with dsRNA containing 8-az... -

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Basic information

Entry
Database: PDB / ID: 9op3
TitleStructure of Human ADAR2-R2D complexed with dsRNA containing 8-azaN and 2'-Deoxy-2'-fluorouridine
Components
  • Double-stranded RNA-specific editase 1
  • RNA 32mer 2F Bottom Strand
  • RNA 32mer Top Strand
KeywordsRNA BINDING PROTEIN/RNA / ADAR / 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 / adenosine to inosine editing / 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 / 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 / neuromuscular process controlling posture / neuromuscular synaptic transmission / innervation / motor neuron apoptotic process / motor behavior / RNA processing / positive regulation of viral genome replication / 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 / metal ion binding / identical protein 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) / Cytokine IL1/FGF / Double-stranded RNA binding motif / 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: 2.59 Å
AuthorsCampbell, K.B. / Ouye, R.B. / Wong, B.L. / Jiang, A. / Okada, K. / McKenney, R.J. / Fisher, A.J. / Beal, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141907 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM149799 United States
CitationJournal: To Be Published
Title: Control of ADAR2 Dimerization and RNA Editing Efficiency by Site-specific 2'-Fluoro Modification of Guide RNAs
Authors: Campbell, K.B. / Ouye, R.B. / Wong, B.L. / Jiang, A. / Okada, K. / McKenney, R.J. / Fisher, A.J. / Beal, P.A.
History
DepositionMay 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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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 32mer Top Strand
D: RNA 32mer 2F Bottom Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,17112
Polymers128,5114
Non-polymers1,6608
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-166 kcal/mol
Surface area42110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.000, 63.210, 142.200
Angle α, β, γ (deg.)90.00, 118.13, 90.00
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 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P78563, double-stranded RNA adenine deaminase

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RNA chain , 2 types, 2 molecules CD

#2: RNA chain RNA 32mer Top Strand


Mass: 10316.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA 32mer 2F Bottom Strand


Mass: 10215.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 67 molecules

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


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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: Reservoir Buffer: 250 mM NaCl, 5 mM MOPS, 20% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2023
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.59→85 Å / Num. obs: 31299 / % possible obs: 93.5 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.8
Reflection shellResolution: 2.59→2.72 Å / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1565 / CC1/2: 0.564 / % possible all: 70

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→65.7 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1573 5.03 %
Rwork0.1776 --
obs0.1799 31294 74.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→65.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 1357 87 59 8075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.158
X-RAY DIFFRACTIONf_dihedral_angle_d20.7143517
X-RAY DIFFRACTIONf_chiral_restr0.0571351
X-RAY DIFFRACTIONf_plane_restr0.0091234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.680.4077320.3859565X-RAY DIFFRACTION16
2.68-2.770.3367830.32451410X-RAY DIFFRACTION40
2.77-2.880.341910.29761835X-RAY DIFFRACTION51
2.88-3.010.30251080.26492233X-RAY DIFFRACTION62
3.01-3.170.28771390.24712712X-RAY DIFFRACTION75
3.17-3.370.26981570.2293122X-RAY DIFFRACTION87
3.37-3.630.25021790.20623524X-RAY DIFFRACTION98
3.63-40.21031890.16583556X-RAY DIFFRACTION99
4-4.570.23281880.14153491X-RAY DIFFRACTION97
4.57-5.760.17262110.14623618X-RAY DIFFRACTION100
5.76-65.70.17651960.14983655X-RAY DIFFRACTION98
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)
11.3253-0.114-0.03931.2155-0.41521.06590.10090.2110.0978-0.1182-0.0817-0.07420.14910.201400.27990.07470.04680.3042-0.05770.2802-28.689513.815526.695
20.2118-0.2257-0.23820.12690.20740.21950.0109-0.01910.07460.21470.03390.0086-0.07010.0792-00.3723-0.00380.02410.27860.00340.3833-40.435629.546944.6474
31.1349-0.03650.09951.45690.2190.79290.04050.0256-0.08730.05780.0236-0.0160.13620.052900.30940.050.00180.2052-0.02050.2576-36.94611.447435.9263
40.13610.05770.03280.5703-0.28280.0638-0.3955-0.5576-0.046-0.48870.5686-0.2433-0.1041-1.0150.01930.63380.0153-0.06951.3740.2070.6183-71.938128.766314.4996
51.96290.6919-0.65990.2779-0.86980.9698-0.0480.10210.0285-0.05660.19520.123-0.0599-0.200500.31710.025-0.02220.47430.07790.4332-79.09619.150735.6464
60.5738-0.3254-0.13550.2750.46070.4948-0.0466-0.0034-0.47940.03910.12830.03660.1373-0.122600.3185-0.0255-0.02850.46380.16470.6016-75.78839.330945.897
73.11070.23450.03260.8005-0.19640.68780.0488-0.4928-0.4657-0.04130.0562-0.0355-0.1286-0.17310.00380.335-0.01460.03410.46460.15180.491-79.528710.624749.6296
8-0.0502-0.08490.06090.34460.1532-0.04610.0999-0.2163-0.1382-0.2612-0.0868-0.0033-0.3765-0.2991-00.48630.0492-0.04180.4421-0.02290.3638-45.106239.592542.7388
90.0148-0.20220.29050.0826-0.53410.3269-0.06790.2062-0.170.13490.5389-0.3990.1138-0.06350.00250.8678-0.0562-0.0781.07190.090.4471-59.153331.1110.9895
10-0.1606-0.04670.10460.1372-0.18380.1140.2095-0.1011-0.2012-0.23920.0243-0.6145-0.413-1.02210.00291.0334-0.129-0.09530.90820.14020.5663-55.704332.77813.6677
110.2448-0.3347-0.31010.537-0.42990.42670.1002-0.1698-0.0833-0.27310.03120.0344-0.6623-0.1702-00.60530.0536-0.02980.3584-0.01090.3133-45.600342.339247.159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 316 through 463 )
2X-RAY DIFFRACTION2chain 'A' and (resid 464 through 501 )
3X-RAY DIFFRACTION3chain 'A' and (resid 502 through 699 )
4X-RAY DIFFRACTION4chain 'B' and (resid 234 through 280 )
5X-RAY DIFFRACTION5chain 'B' and (resid 281 through 415 )
6X-RAY DIFFRACTION6chain 'B' and (resid 416 through 531 )
7X-RAY DIFFRACTION7chain 'B' and (resid 532 through 700 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 16 )
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 32 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'D' and (resid 17 through 32 )

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