[English] 日本語
Yorodumi
- PDB-9d5k: Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsR... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
Components

-
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)

-
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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more