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- EMDB-70641: Monomeric ADAR2_E488Q bound to dsRNA sequence derived from human ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70641
TitleMonomeric ADAR2_E488Q bound to dsRNA sequence derived from human GLI1 gene
Map datamain
Sample
  • Complex: RNA derived from GLI1 dsRNA in complex with ADAR2
    • Protein or peptide: Double-stranded RNA-specific editase 1 (ADAR2)
    • RNA: GLI1-61bp, edited strand
    • RNA: GLI1-61bp, non-edited strand
Keywordsprotein:RNA complex / RNA editing / ADAR / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsMatthews MM / Wolf M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K15050 Japan
CitationJournal: To Be Published
Title: Structures of human ADAR2 reveal the effects of dsRNA helical defects on binding and editing specificity
Authors: Matthews MM / Mozumder S / Mello Y / Campbell KB / Cheng J / Shiraj A / Shweta H / Mendoza HG / Spencer B / Jauregui-Matos V / Goldman YE / Beal PA / Fisher AJ / Wolf M
History
DepositionMay 15, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70641.png

Downloads & links

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Map

FileDownload / File: emd_70641.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 128 pix.
= 281.6 Å		2.2 Å/pix.
x 128 pix.
= 281.6 Å		2.2 Å/pix.
x 128 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.29
Minimum - Maximum-1.6917471 - 5.7664533
Average (Standard dev.)-0.0032736987 (±0.19293173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70641_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_70641_half_map_1.map
AnnotationhalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfA

Fileemd_70641_half_map_2.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA derived from GLI1 dsRNA in complex with ADAR2

EntireName: RNA derived from GLI1 dsRNA in complex with ADAR2
Components
  • Complex: RNA derived from GLI1 dsRNA in complex with ADAR2
    • Protein or peptide: Double-stranded RNA-specific editase 1 (ADAR2)
    • RNA: GLI1-61bp, edited strand
    • RNA: GLI1-61bp, non-edited strand

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Supramolecule #1: RNA derived from GLI1 dsRNA in complex with ADAR2

SupramoleculeName: RNA derived from GLI1 dsRNA in complex with ADAR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 115 KDa

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Macromolecule #1: Double-stranded RNA-specific editase 1 (ADAR2)

MacromoleculeName: Double-stranded RNA-specific editase 1 (ADAR2) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: double-stranded RNA adenine deaminase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSHHHHHHHH HHHHENLYFQ GDIEDEENMS SSSTDVKENR NLDNVSPKDG STPGPGEGSQ LSNGGGGGPG RKRPLEEGSN GHSKYRLKK RRKTPGPVLP KNALMQLNEI KPGLQYTLLS QTGPVHAPLF VMSVEVNGQV FEGSGPTKKK AKLHAAEKAL R SFVQFPNA ...String:
MSHHHHHHHH HHHHENLYFQ GDIEDEENMS SSSTDVKENR NLDNVSPKDG STPGPGEGSQ LSNGGGGGPG RKRPLEEGSN GHSKYRLKK RRKTPGPVLP KNALMQLNEI KPGLQYTLLS QTGPVHAPLF VMSVEVNGQV FEGSGPTKKK AKLHAAEKAL R SFVQFPNA SEAHLAMGRT LSVNTDFTSD QADFPDTLFN GFETPDKAEP PFYVGSNGDD SFSSSGDLSL SASPVPASLA QP PLPVLPP FPPPSGKNPV MILNELRPGL KYDFLSESGE SHAKSFVMSV VVDGQFFEGS GRNKKLAKAR AAQSALAAIF NLH LDQTPS RQPIPSEGLQ LHLPQVLADA VSRLVLGKFG DLTDNFSSPH ARRKVLAGVV MTTGTDVKDA KVISVSTGTK CING EYMSD RGLALNDCHA EIISRRSLLR FLYTQLELYL NNKDDQKRSI FQKSERGGFR LKENVQFHLY ISTSPCGDAR IFSPH EPIL EEPADRHPNR KARGQLRTKI ESGQGTIPVR SNASIQTWDG VLQGERLLTM SCSDKIARWN VVGIQGSLLS IFVEPI YFS SIILGSLYHG DHLSRAMYQR ISNIEDLPPL YTLNKPLLSG ISNAEARQPG KAPNFSVNWT VGDSAIEVIN ATTGKDE LG RASRLCKHAL YCRWMRVHGK VPSHLLRSKI TKPNVYHESK LAAKEYQAAK ARLFTAFIKA GLGAWVEKPT EQDQFSLT P

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Macromolecule #2: GLI1-61bp, edited strand

MacromoleculeName: GLI1-61bp, edited strand / type: rna / ID: 2
Details: "top" strand of 61bp dsRNA sequence, including a 3prime Cy5 tag
Source (natural)Organism: Homo sapiens (human)
SequenceString:
AGCAAGUCCA CGUGCAUGGC UCGCGAUGCU (8AZ)GAGGGCUCU GAUAGCGGAU GGACAUCGAC G(CY5)

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Macromolecule #3: GLI1-61bp, non-edited strand

MacromoleculeName: GLI1-61bp, non-edited strand / type: rna / ID: 3
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGUCGAUGUC CAUCCGCUAU CAGAGCCCCC CAGCAUCGCG AGCCAUGCAC GUGGACUUGC U

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
15.0 mMTris
140.0 mMpotassium chlorideKCl
10.0 mMsodium chlorideNaCl
1.0 mMmagnesium chlorideMgCl2
0.5 mMEDTA
0.003 %NP 40
1.0 mMbeta mercapto ethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 14491 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 166332
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 159522 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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