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- EMDB-64013: The structure of type III CRISPR-associated deaminase in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64013
TitleThe structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5
Map data
Sample
  • Complex: The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 1
    • Protein or peptide: adenosine deaminase
  • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordsdeaminase / complex / ATP / HYDROLASE/RNA / HYDROLASE-RNA complex
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / hypoxanthine salvage / adenosine deaminase activity / metal ion binding / cytosol
Similarity search - Function
CRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
Biological speciesThermoanaerobaculum aquaticum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsKong JP / Wu WQ / Li ZX / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82473977 China
CitationJournal: To Be Published
Title: The structure of type III CRISPR-associated deaminase
Authors: Kong JP / Wu WQ / Li ZX / Xiao YB
History
DepositionApr 3, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64013.png

Downloads & links

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Map

FileDownload / File: emd_64013.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.35776296 - 0.7384157
Average (Standard dev.)0.00024267554 (±0.020945609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64013_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_64013_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64013_half_map_2.map
Projections & Slices
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Sample components

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Entire : The structure of type III CRISPR-associated deaminase in complex ...

EntireName: The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 1
Components
  • Complex: The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 1
    • Protein or peptide: adenosine deaminase
  • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The structure of type III CRISPR-associated deaminase in complex ...

SupramoleculeName: The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)

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Macromolecule #1: adenosine deaminase

MacromoleculeName: adenosine deaminase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: adenosine deaminase
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Molecular weightTheoretical: 70.328023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRILLCSVGT SWAVVPEAMQ LLGSQGFDEV HVLTTASSKI SPGVEQLLRY FEMHPGPRFS ISRVQDFEDL RSEQDHMLFE EVLWRWLLQ RAPQAAHRYI CLAGGYKTIS AAMQRAAALF GACEVFHVLC EPRFGPQGNR EASTLEEVEQ AIATNALRFV R LGPEPGWP ...String:
MRILLCSVGT SWAVVPEAMQ LLGSQGFDEV HVLTTASSKI SPGVEQLLRY FEMHPGPRFS ISRVQDFEDL RSEQDHMLFE EVLWRWLLQ RAPQAAHRYI CLAGGYKTIS AAMQRAAALF GACEVFHVLC EPRFGPQGNR EASTLEEVEQ AIATNALRFV R LGPEPGWP QLRLLSAPSF PLESTLQGPV HWVRASDMRL RQHVEGVLER SRHILAAWEG ISELPIPALA AWPPSHLRWL HE PLDPVQD KAWVQALPKV ELHCHLGGFA THGELLHKVR QEAANPESLP PVRAIPLPPG WPIPEEPIGL ERYMRLGDNN GSA LLKDPG CLRAQCRLLY EALLADHVAY AEIRCSPANY ASASRSPWVV LQEIRNHFQQ AMEETPEDRR CHVNLLLTAT REEG GDRSR IARHLALAIT AAEHWKNGCR VVGVDLAGFE DRTTRAAMFA TDFEPVHRVG LAVTVHAGEN DDVEGIWQAV FKLSA RRLG HALHLSRSPD LLRVVAERGI AVELCPYANL QIKGFPLDEE QEGSETYPLR GYLAAGVAVT LNTDNLGISQ ASLTDN LLL TARLCPGITR LEVLKTQVFA AQAAFANQAE RKALWARLAQ VPVPTDTEQK NGNDAKASHQ PRHHHHHH

UniProtKB: adenosine deaminase

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Macromolecule #2: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 3
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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 / Nominal defocus max: 2.4 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106481
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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