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- PDB-9d5j: Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsR... -

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Basic information

Entry
Database: PDB / ID: 9d5j
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing deoxyinosine at the -1 position of the guide strand
Components
  • Isoform 4 of Double-stranded RNA-specific editase 1
  • RNA Bottom Strand containing deoxyinosine complementary to a guanosine adjacent to the target site
  • RNA Top Strand Containing 8-azanebularine (8AZ)
KeywordsRNA BINDING PROTEIN/RNA / Adenosine Deaminase / dsRNA / Complex / RNA editing / deoxyinosine / 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 / adenosine deaminase activity / neuromuscular synaptic transmission / innervation / motor neuron apoptotic process / motor behavior / 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 / 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 / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / 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. / Cheng, J. / Manjunath, A. / Campbell, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM149799 United States
Other privateProQR
CitationJournal: Biomolecules / Year: 2024
Title: Nucleoside Analogs in ADAR Guide Strands Enable Editing at 5'-G A Sites.
Authors: Manjunath, A. / Cheng, J. / Campbell, K.B. / Jacobsen, C.S. / Mendoza, H.G. / Bierbaum, L. / Jauregui-Matos, V. / Doherty, E.E. / Fisher, A.J. / Beal, P.A.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 4 of Double-stranded RNA-specific editase 1
B: Isoform 4 of Double-stranded RNA-specific editase 1
C: RNA Top Strand Containing 8-azanebularine (8AZ)
D: RNA Bottom Strand containing deoxyinosine complementary to a guanosine adjacent to the target site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,05611
Polymers128,4194
Non-polymers1,6377
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-151 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.694, 63.130, 141.778
Angle α, β, γ (deg.)90.000, 118.232, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / RNA chain / DNA/RNA hybrid , 3 types, 4 molecules ABCD

#1: Protein Isoform 4 of Double-stranded RNA-specific editase 1 / RNA-editing deaminase 1 / RNA-editing enzyme 1 / dsRNA adenosine deaminase


Mass: 53932.664 Da / Num. of mol.: 2 / Fragment: residues 215-701 / 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
#2: RNA chain RNA Top Strand Containing 8-azanebularine (8AZ)


Mass: 10355.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA/RNA hybrid RNA Bottom Strand containing deoxyinosine complementary to a guanosine adjacent to the target site


Mass: 10198.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 22 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM MOPS pH 7.0, 100 mM sodium chloride, 9% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2024
RadiationMonochromator: Liquid nitrogen-cooled double crystal, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→49.6 Å / Num. obs: 21944 / % possible obs: 89.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 69.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.06 / Rrim(I) all: 0.115 / Net I/σ(I): 7.4
Reflection shellResolution: 2.8→3.081 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1097 / CC1/2: 0.602 / Rpim(I) all: 0.519 / Rrim(I) all: 1.001 / % possible all: 48.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.6 Å / SU ML: 0.2784 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.8961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 1091 4.97 %
Rwork0.188 20848 -
obs0.1904 21939 64.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6559 1359 86 15 8019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00858290
X-RAY DIFFRACTIONf_angle_d1.136811529
X-RAY DIFFRACTIONf_chiral_restr0.05231347
X-RAY DIFFRACTIONf_plane_restr0.00931231
X-RAY DIFFRACTIONf_dihedral_angle_d20.25563510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.930.5455120.3452177X-RAY DIFFRACTION4.54
2.93-3.090.2906480.298915X-RAY DIFFRACTION22.99
3.09-3.280.3047900.27511903X-RAY DIFFRACTION47.75
3.28-3.530.29451450.24252673X-RAY DIFFRACTION66.81
3.53-3.890.24491580.19233339X-RAY DIFFRACTION83.58
3.89-4.450.21062060.17463796X-RAY DIFFRACTION94.97
4.45-5.610.20892290.17323997X-RAY DIFFRACTION99.62
5.61-49.60.23842030.17294048X-RAY DIFFRACTION97.57
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)
11.146777890540.534356070678-0.1796520844531.38907325791-0.3411560600431.091742643320.01847360514370.1340995629230.0849136505354-0.0846638586018-0.0829226463027-0.09495317799260.1205971141750.1351304159938.36408652553E-60.3150986687690.08562822285040.06530269130260.279450734815-0.02983615999460.263160579741-29.725070341845.255351562927.2321278625
20.29646120573-0.424187945157-0.09094669509990.4369861130630.0239070867380.0386426084468-0.0510493515383-0.09868444424710.4304298227630.204603697946-0.01423522334630.167188223728-0.277863416472-0.1130276749239.64119542621E-50.394342496081-0.01813666051360.007071311866820.287452086283-0.03152195266930.478417560537-37.784958639363.994126359743.6361834692
31.29696648427-0.389372278056-0.007872414969230.9402744939460.108520165450.7608759507140.01077863914120.053360513308-0.1308696264260.06102625670640.03463298657660.04605694251370.03217183669850.08288451653522.13335549798E-50.352748281520.00430487507976-0.01189360091130.234885385554-0.02083522791920.226787114642-37.96976552342.946093975936.2145857533
40.191455131509-0.3758032998270.2186561011770.248186838445-0.172302324510.105384352153-0.0292028753117-0.0368159387932-0.0345785941593-0.3308594851770.430749883111-0.0503603043868-0.240076882503-0.8415690254571.50908489652E-50.681449443397-0.0147878037979-0.1134862533591.279423258070.1946370651740.783380475825-73.8250034757.001482739614.377684646
51.421767219490.2147764307290.137374766838-0.08468154093220.1078113570330.3421175851110.03209578861520.00859621760973-0.191561912679-0.06815854643090.09349719970340.0814927996232-0.102644678993-0.175129656075-5.66300361099E-50.2608542003750.0116804134122-0.02297081541960.4824010947180.1196619568720.507465448498-82.698935978947.617482420440.374517015
60.02674787961260.05016113540610.06425484568290.03864360592820.07305574847460.0493719468296-0.371813925828-0.348588737422-0.3169743766420.1229706519870.134801527487-0.1070919356240.1441143910090.463982319613-5.2676759542E-50.6858596575670.0753794407794-0.10569083820.5762575699870.1931117724230.639532526943-62.276823851441.275549922557.6696145316
71.99761736222-0.06154222017250.2323539517451.053907531990.2758938150560.6305001397610.0580884730293-0.31220692731-0.2926026904970.02906681682530.111243527473-0.0324350445396-0.0135734550906-0.194158899544-1.78525643062E-50.35368295901-0.02280280588960.03186260930670.4683101045790.1309119512320.479130399013-80.733792795242.116258234849.4451525196
80.4224647334020.0989592933966-0.52782458270.7242195695090.003084262065540.1515793321940.0325653541704-0.152994661412-0.207564075785-0.3853538867290.0783363202108-0.0958873733216-0.502168279216-0.2462705793621.25653757119E-50.5673306077220.0292906911305-0.08568830405670.4257727059760.02053933609440.407595859254-45.931849806570.971510660642.7378932608
90.07388996297480.03969413902580.173851450794-0.0959908575844-0.3055998574150.323741615796-0.1100270820690.402274163064-0.3560023942020.02143836024150.466222300345-0.355141972165-0.3556496651570.2757792820017.62878951243E-50.869513085996-0.0142085136002-0.05597670304521.152077079220.08120825821090.644915185433-60.619946530562.82997766980.935416693321
100.1099764260460.391324457836-0.1808067248910.292563029397-0.1571587572450.1853696148060.001052272077520.0413333090104-0.4079062890270.04449749690970.102993725122-0.590516071503-0.796908422212-1.036788365970.0001885412331341.18157384138-0.0593354290299-0.05492134608941.013188927980.1804264923450.729898731726-57.211805071764.47266152933.45608897315
110.165955764008-0.3632356948950.08665827399580.47680767508-0.123883835778-0.00712178785521-0.152655364793-0.341333762064-0.215653813501-0.3018679714450.1629782668070.0173534696051-0.694144039463-0.14347487471-0.01115839202270.6553984902570.109172272941-0.02369655546850.361805803711-0.02944314603630.402389408899-46.445896348173.698715035447.3021268354
120.122727375687-0.141613944929-0.002755174047310.190702512144-0.04478353460370.0748426228689-0.451317420937-0.3944428647150.001368079587640.4827604261270.124726260013-0.03675025942320.247221765053-0.428236015367-0.03855698527271.031157020140.0637608083457-0.1042429163180.0804445624310.4117789490750.0717810956796-49.646927750752.432296998648.3442596107
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 316 through 463 )AA316 - 4631 - 148
22chain 'A' and (resid 464 through 491 )AA464 - 491149 - 176
33chain 'A' and (resid 501 through 699 )AA501 - 699186 - 384
44chain 'B' and (resid 235 through 303 )BD235 - 3031 - 69
55chain 'B' and (resid 304 through 485 )BD304 - 48570 - 239
66chain 'B' and (resid 486 through 512 )BD486 - 512240 - 266
77chain 'B' and (resid 513 through 700 )BD513 - 700267 - 454
88chain 'C' and (resid 1 through 16 )CH1 - 16
99chain 'C' and (resid 17 through 32 )CH17 - 32
1010chain 'D' and (resid 1 through 16 )DI1 - 16
1111chain 'D' and (resid 17 through 32 )DI - K17 - 32
1212chain 'A' and (resid 492 through 500 )AA492 - 500177 - 185

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