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- EMDB-70417: CryoEM structure of Cad1 in App form, symmetry expanded dimer, re... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70417
TitleCryoEM structure of Cad1 in App form, symmetry expanded dimer, refined against a composite map
Map data
Sample
  • Complex: Cad1
    • Protein or peptide: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
  • Ligand: ZINC ION
KeywordsCRISPR-associated Rossman-fold (CARF) / ATP deaminase / CRISPR immunity / cooperative activation / IMMUNE SYSTEM / HYDROLASE
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / hypoxanthine salvage / adenosine deaminase activity / adenosine catabolic process / 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: 2.7 Å
AuthorsZhao Y / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152081 United States
CitationJournal: To Be Published
Title: Sequential Conformational Activation of a CARF-Fused Adenosine Deaminase by Cyclic Oligoadenylates
Authors: Zhao Y / Li H
History
DepositionApr 29, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70417.png

Downloads & links

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Map

FileDownload / File: emd_70417.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.58
Minimum - Maximum-3.8937602 - 11.620214000000001
Average (Standard dev.)0.06448606 (±0.18607761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cad1

EntireName: Cad1
Components
  • Complex: Cad1
    • Protein or peptide: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
  • Ligand: ZINC ION

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Supramolecule #1: Cad1

SupramoleculeName: Cad1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)

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Macromolecule #1: CRISPR-associated ring nuclease and adenosine deaminase, subunit A

MacromoleculeName: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: adenosine deaminase
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Molecular weightTheoretical: 69.499133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 PR

UniProtKB: adenosine deaminase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8200000000000001 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 938192
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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