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- EMDB-60041: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60041
TitleCryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex
Map data
Sample
  • Complex: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex
    • Protein or peptide: Adr-2-binding protein 1
    • Protein or peptide: Double-stranded RNA-specific adenosine deaminase adr-2
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
Keywordsadenosine deaminase / RNA BINDING PROTEIN
Function / homology
Function and homology information


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 / adenosine deaminase activity / positive regulation of chemotaxis / RNA processing / determination of adult lifespan ...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 / adenosine deaminase activity / positive regulation of chemotaxis / RNA processing / determination of adult lifespan / positive regulation of protein localization to nucleus / mRNA processing / chemotaxis / double-stranded RNA binding / nucleolus / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Adr-2-binding protein 1 / Double-stranded RNA-specific adenosine deaminase adr-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLiu ZM / Mu JQ / Wu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex
Authors: Liu ZM / Mu JQ / Wu C
History
DepositionMay 6, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60041.png

Downloads & links

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Map

FileDownload / File: emd_60041.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 288 pix.
= 246.528 Å		0.86 Å/pix.
x 288 pix.
= 246.528 Å		0.86 Å/pix.
x 288 pix.
= 246.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-3.0743282 - 5.929618
Average (Standard dev.)0.00047440702 (±0.09478075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 246.528 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_60041_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60041_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60041_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex

EntireName: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex
Components
  • Complex: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex
    • Protein or peptide: Adr-2-binding protein 1
    • Protein or peptide: Double-stranded RNA-specific adenosine deaminase adr-2
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex

SupramoleculeName: Cryo-EM structure of Adr-2-Adbp-1-dsRBD1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Adr-2-binding protein 1

MacromoleculeName: Adr-2-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 23.986254 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSFASGCTPV SFDKLFEVSS GDKVSRENWG MIARPEPQHD SLKRRNTTSS IAKKKAKMTR GDEQITDETA RKAATQLLDQ IQDTPGRIS LNFETPEAAS VCPIPTSLNQ IVNTKWTVNQ LQEGQLTMLL AQDANKFKSL GVKNIKKGSV ETQILPRQMD V KEIVEKLK ...String:
MSFASGCTPV SFDKLFEVSS GDKVSRENWG MIARPEPQHD SLKRRNTTSS IAKKKAKMTR GDEQITDETA RKAATQLLDQ IQDTPGRIS LNFETPEAAS VCPIPTSLNQ IVNTKWTVNQ LQEGQLTMLL AQDANKFKSL GVKNIKKGSV ETQILPRQMD V KEIVEKLK KQDNDSDQFV GYAAAVANVL RRCDAETAQK ITQAITATIE KEAPSIVNC

UniProtKB: Adr-2-binding protein 1

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Macromolecule #2: Double-stranded RNA-specific adenosine deaminase adr-2

MacromoleculeName: Double-stranded RNA-specific adenosine deaminase adr-2
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: double-stranded RNA adenine deaminase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 55.39159 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVEEGMEVE LKSEKMDLDD NIPDFVKETV ERSGKNPMSL FSELYVHMTG NTPVFDFYNR NQPNGSMKFI CVVILNGERI EGNVKSKKK EAKVSCSLKG LEVVLKHVSE YVVPAVKFEE KTTFFEMLRE HTYAKFYELC KNNALIYGFE KVIASVFLKI N GNLQIIAL ...String:
MSVEEGMEVE LKSEKMDLDD NIPDFVKETV ERSGKNPMSL FSELYVHMTG NTPVFDFYNR NQPNGSMKFI CVVILNGERI EGNVKSKKK EAKVSCSLKG LEVVLKHVSE YVVPAVKFEE KTTFFEMLRE HTYAKFYELC KNNALIYGFE KVIASVFLKI N GNLQIIAL STGNKGLRGD KIVNDGTALI DCHAEILARR GLLRFLYSEV LKFSTEPPNS IFTKGKNALV LKPGISFHLF IN TAPCGVA RIDKKLKPGT SDDLQNSSRL RFKIDKGMGT VLGGASEFEA PQTFDGIMMG ERMRTMSCSD KLLRANVLGV QGA ILSHFI DPIYYSSIAV AELNNADRLR KAVYSRAATF KPPAPFHVQD VEIGECQVED TEQSTSAAAR STISSMNWNL ADGN TEVVR TSDGMVHDKD MSGADITTPS RLCKKNMAEL MITICTLTKT SVDYPISYEE LKAGSQEYAA AKKSFITWLR QKDLG IWQR KPREFQMFTI N

UniProtKB: Double-stranded RNA-specific adenosine deaminase adr-2

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Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136807
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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