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- PDB-9d5k: Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsR... -

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Basic information

Entry
Database: PDB / ID: 9d5k
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing an expanded cytidine analog at the -1 position of the guide strand
Components
  • Isoform 4 of Double-stranded RNA-specific editase 1
  • RNA Bottom Strand
  • RNA Top Strand
KeywordsRNA BINDING PROTEIN/RNA / Adenosine Deaminase / dsRNA / Complex / RNA editing / cytidine analog / 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 / 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 / tRNA-specific adenosine deaminase activity / adenosine to inosine editing / 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 deaminase activity / 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 / 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 / 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: 2.697 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
D: RNA Bottom Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9339
Polymers128,4584
Non-polymers1,4755
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-164 kcal/mol
Surface area43010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.775, 63.112, 141.064
Angle α, β, γ (deg.)90.000, 118.538, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 316 through 328 or resid 330...
d_2ens_1(chain "B" and (resid 316 through 328 or resid 330 through 699 or resid 801 through 802))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNSERSERAA316 - 328102 - 114
d_12LEULEUILEILEAA330 - 463116 - 249
d_13ALAALAASNASNAA476 - 496262 - 282
d_14GLUGLULEULEUAA509 - 699295 - 485
d_15IHPIHPIHPIHPAE801
d_21GLNGLNSERSERBB316 - 328102 - 114
d_22LEULEULEULEUBB330 - 699116 - 485
d_23IHPIHPIHPIHPBH801

NCS oper: (Code: givenMatrix: (-0.566426017942, 0.80366903184, 0.182421636489), (-0.204966393588, 0.0770176687178, -0.975734111428), (-0.798216977831, -0.59007149225, 0.121100331692)Vector: 18. ...NCS oper: (Code: given
Matrix: (-0.566426017942, 0.80366903184, 0.182421636489), (-0.204966393588, 0.0770176687178, -0.975734111428), (-0.798216977831, -0.59007149225, 0.121100331692)
Vector: 18.4102082964, 56.5592921002, 92.0003540344)

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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


Mass: 10355.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: strand bearing 8-azanebularine (8AZ) / Source: (synth.) Homo sapiens (human)
#3: DNA/RNA hybrid RNA Bottom Strand


Mass: 10237.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: with base-expanded cytidine analog (A1BBA) complementary to a guanosine adjacent to the target site
Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 39 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 50 mM MOPS pH 7.0, 100 mM NaCl, 10% PEG 4000

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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: Apr 25, 2024
RadiationMonochromator: Liquid / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→61.962 Å / Num. obs: 27371 / % possible obs: 92 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 79.89 Å2 / CC1/2: 0.897 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Net I/σ(I): 10.3
Reflection shellResolution: 2.69→2.879 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1369 / CC1/2: 0.704 / Rpim(I) all: 0.392 / Rrim(I) all: 0.739 / % possible all: 64.4

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.697→49.46 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 35.5211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2683 3495 4.93 %
Rwork0.2209 67333 -
obs0.2234 27371 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.67 Å2
Refinement stepCycle: LAST / Resolution: 2.697→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 1362 75 34 7945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01348206
X-RAY DIFFRACTIONf_angle_d1.634611420
X-RAY DIFFRACTIONf_chiral_restr0.07471335
X-RAY DIFFRACTIONf_plane_restr0.01171216
X-RAY DIFFRACTIONf_dihedral_angle_d19.47693480
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.17250121086 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.697-2.730.46221360.45982269X-RAY DIFFRACTION80.76
2.73-2.770.5241460.44122661X-RAY DIFFRACTION98.42
2.77-2.810.4371490.43322814X-RAY DIFFRACTION98.34
2.81-2.850.40451490.40442690X-RAY DIFFRACTION97.56
2.86-2.90.40031670.38742679X-RAY DIFFRACTION98.07
2.9-2.950.32841460.35682707X-RAY DIFFRACTION97.94
2.95-3.010.35861580.33782789X-RAY DIFFRACTION97.71
3.01-3.060.37871190.33252675X-RAY DIFFRACTION97.49
3.06-3.130.36831130.30512720X-RAY DIFFRACTION96.85
3.13-3.190.33291170.29932678X-RAY DIFFRACTION96.58
3.19-3.270.34151630.28042522X-RAY DIFFRACTION91.61
3.27-3.350.3381310.2912699X-RAY DIFFRACTION96.13
3.35-3.440.32111290.26772771X-RAY DIFFRACTION98.04
3.44-3.540.29861320.23012722X-RAY DIFFRACTION98.48
3.54-3.660.26421240.22132753X-RAY DIFFRACTION98.33
3.66-3.790.22821480.20762768X-RAY DIFFRACTION98.68
3.79-3.940.25571540.20592719X-RAY DIFFRACTION98.32
3.94-4.120.30261150.21772746X-RAY DIFFRACTION98.52
4.12-4.330.26551550.19682713X-RAY DIFFRACTION98.35
4.33-4.610.22531430.1762756X-RAY DIFFRACTION97.81
4.61-4.960.18761200.17982547X-RAY DIFFRACTION91.4
4.96-5.460.26231340.19742788X-RAY DIFFRACTION99.25
5.46-6.250.27771570.19922760X-RAY DIFFRACTION99.25
6.25-7.870.25511430.2072758X-RAY DIFFRACTION98.84
7.87-49.460.1911470.15232629X-RAY DIFFRACTION95.23
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)
12.25197390980.210420236666-0.3649525167181.61904705453-0.2450570732541.30376295690.07779639563060.1196106852850.213506795217-0.315014163902-0.0316884328394-0.3780526178790.06394876543190.09602449698743.58306128567E-50.7006091081580.05359912082870.1182499902980.759548917605-0.02380637238830.66302242227157.67053645515.455417941627.0642587445
20.654959648231-0.529971380014-0.03287970384110.426914350624-0.28345370427-0.0646919467063-0.126892070190.1799132986060.5217402310520.9080331204710.2405313185790.20852403511-0.19013375108-0.2637624291990.0006450620708250.8654074961320.0131885631766-0.01949692757250.672717278957-0.01284279883880.6634910592846.070481485431.33493970244.3579660693
32.07215780801-0.565464221226-0.04646765718911.986060911770.6608417131041.72142142321-0.01320142726990.1039258886890.1051284772440.1469806002930.0980747667711-0.0920221194995-0.1181237460340.108009753522-0.0001102349833330.6781086458010.02321494097380.009823606975770.589913641079-0.001990467155180.58553711577252.368869995719.265619539835.1305270523
41.32734000042-0.372642704936-0.2317208680290.4014820019140.275541441886-0.07914835922050.244560680150.103354597616-0.2530525798610.2399315399870.0691536323590.1034370000360.1822812279570.1399307510568.26146599286E-51.015842713590.064424670359-0.1064040025790.674429332402-0.03076156755440.71936318517545.16992672414.8760504039337.1234265013
5-0.256270240533-0.08407395612780.03477599441520.06506556046280.1365418046280.0489880768261-0.326747893827-0.3163974227960.1750694035370.1993399292310.1861063792590.787457791311-0.245631651134-0.630304412737-7.52793961268E-61.31040370821-0.0673803189025-0.1999217899291.591644154960.1584569065671.5229948636313.305508231325.567394152715.0932579013
60.2676259465760.1709638575851.21122762360.695075054701-1.111495487521.38785046261-0.1234583844330.194469889054-0.05314407660190.131221664940.4409037398480.508754166423-0.03345521563310.05542042795440.2854133280420.8147579215940.1072392274120.09838481363351.037336763450.2254160251471.316621765814.7266429375521.938553316740.2414911191
70.7347247990710.2862297948550.5304398787170.7924087024321.043230326710.6795308619610.134174413253-0.0435408900772-0.1539937402970.0008712119005150.2027007859970.08268642932420.469211487475-0.2482845876870.1464500076040.662467978955-0.0651462875453-0.05005460089750.9312717331430.2093644012590.9938143277288.3728344858211.30009129343.02930279
81.896018817-0.6712837323320.2757019604310.5232739392310.9359598172960.6928476068-0.0290919642216-0.285015891385-0.3133417339460.03855052721570.1349120081460.17140686843-0.00799210673189-0.2533970831314.13375314197E-50.8652849696410.01016682795690.1858941391930.9564193446720.192184551381.088231907236.2124077961512.560346569248.8863657621
90.981713300013-0.798160571427-1.161243261791.191520809940.168992245350.109474499301-0.08923771483730.101758539418-0.190550881068-0.3436482565390.219374137975-0.0381585351998-1.03473363016-0.1327222474083.18948592854E-61.07372874653-0.0122207279995-0.06408485795290.7631370949490.06059657187330.9045303596841.292215497841.236254650942.2683908836
10-0.090153885095-0.1295034532450.149022327916-0.106166018495-0.359441184030.3868651289020.06561624849530.388019899552-0.404431170829-0.06779374241670.363165392115-0.838505425262-0.700703994385-0.0453882871777-0.0008399055886531.56385883866-0.08698223220710.01091061079841.761608282650.1133218085711.1706012941926.73480566632.90624604820.524085254788
110.356716085282-0.0801094315695-0.03015019892030.493698227486-0.1603843874630.3638922665440.239127131514-0.0306442930841-0.2749903409340.0551174156779-0.173141337651-1.19874812996-0.902394789417-1.06141679761-0.0005584373729092.04695077286-0.1424740419770.03659720533071.538648016790.124069944451.5190508469530.188807961234.46336660913.12451827077
12-0.0089321879723-0.370238917497-0.01191268051330.616742915358-0.112356606407-0.0264220193451-0.122232508193-0.34575757243-0.180543258339-0.5605691462960.1063831096750.101985710361-0.901951435377-0.288164614610.0001757856232741.224669690890.130976919633-0.06196435317440.842883412081-0.06508637173460.88478971463740.718135429743.957463226946.7399383152
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 501 )AA464 - 501149 - 186
33chain 'A' and (resid 502 through 617 )AA502 - 617187 - 302
44chain 'A' and (resid 618 through 699 )AA618 - 699303 - 384
55chain 'B' and (resid 235 through 310 )BD235 - 3101 - 76
66chain 'B' and (resid 311 through 415 )BD311 - 41577 - 181
77chain 'B' and (resid 416 through 531 )BD416 - 531182 - 273
88chain 'B' and (resid 532 through 700 )BD532 - 700274 - 442
99chain 'C' and (resid 1 through 16 )CG1 - 16
1010chain 'C' and (resid 17 through 32 )CG17 - 32
1111chain 'D' and (resid 1 through 16 )DH1 - 16
1212chain 'D' and (resid 17 through 32 )DH - J17 - 32

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