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- PDB-7kfn: Structure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bo... -

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Basic information

Entry
Database: PDB / ID: 7kfn
TitleStructure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA containing a 2'-deoxy Benner's Base Z opposite the edited base
Components
  • Double-stranded RNA-specific editase 1
  • Gli1 1W5 23mer RNA
  • Gli1 8AZ 23mer RNA
KeywordsRNA BINDING PROTEIN/RNA / 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 / adenosine to inosine editing / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity ...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 / adenosine to inosine editing / 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 / 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 / nucleus / metal ion binding / 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: 2.5 Å
AuthorsWilcox, X.E. / Fisher, A.J. / Beal, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM061115 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position.
Authors: Doherty, E.E. / Wilcox, X.E. / van Sint Fiet, L. / Kemmel, C. / Turunen, J.J. / Klein, B. / Tantillo, D.J. / Fisher, A.J. / Beal, P.A.
History
DepositionOct 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Gli1 8AZ 23mer RNA
C: Gli1 1W5 23mer RNA
D: Double-stranded RNA-specific editase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2418
Polymers104,7904
Non-polymers1,4514
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-144 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.024, 63.612, 132.149
Angle α, β, γ (deg.)90.000, 126.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AD

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


Mass: 45005.383 Da / Num. of mol.: 2
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 BC

#2: RNA chain Gli1 8AZ 23mer RNA


Mass: 7415.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Generated by solid phase oligonucleotide synthesis / Source: (synth.) Homo sapiens (human)
#3: RNA chain Gli1 1W5 23mer RNA


Mass: 7363.482 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, 256 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.76 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES:NaOH pH 6.5, 18% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→105.86 Å / Num. obs: 39692 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Net I/σ(I): 8.7 / Num. measured all: 152256 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.63.80.6131661044220.7140.360.7142.299.1
9.01-105.863.70.0533259080.9950.0290.05820.399.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Aimless0.7.4data scaling
XDSJan 31, 2020data processing
PHASER2.7.18phasing
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D06

6d06


Resolution: 2.5→68.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.696 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1907 4.8 %RANDOM
Rwork0.1707 ---
obs0.1733 37774 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.17 Å2 / Biso mean: 46.536 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.5→68.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 977 74 252 7107
Biso mean--41.01 42.17 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176086
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6059821
X-RAY DIFFRACTIONr_angle_other_deg1.2671.69114152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5415737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42320.74311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.873151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7051552
X-RAY DIFFRACTIONr_chiral_restr0.0730.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021536
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 153 -
Rwork0.274 2747 -
all-2900 -
obs--98.51 %

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