[English] 日本語
Yorodumi
- EMDB-45241: cryoEM structure of CRISPR associated effector, CARF-Adenosine de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45241
TitlecryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in apo form
Map dataz-fliped main map
Sample
  • Complex: apo Cad1 (CRISPR associated Adenosine deaminase 1) full length protein
    • Protein or peptide: Adenosine deaminase domain-containing protein
  • Ligand: MAGNESIUM ION
KeywordsAntiphage defense / CRISPR / Deamination / CARF-Adenosine deaminase / ANTIVIRAL PROTEIN
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 speciesBacteriodale bacterium (bacteria) / Bacteroidales bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMajumder P / Patel DJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIHGM 129430, NIHGM 145888 United States
CitationJournal: Cell / Year: 2024
Title: The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity.
Authors: Christian F Baca / Puja Majumder / James H Hickling / Linzhi Ye / Marianna Teplova / Sean F Brady / Dinshaw J Patel / Luciano A Marraffini /
Abstract: Type III CRISPR systems provide immunity against genetic invaders through the production of cyclic oligo-adenylate (cA) molecules that activate effector proteins that contain CRISPR-associated ...Type III CRISPR systems provide immunity against genetic invaders through the production of cyclic oligo-adenylate (cA) molecules that activate effector proteins that contain CRISPR-associated Rossman fold (CARF) domains. Here, we characterized the function and structure of an effector in which the CARF domain is fused to an adenosine deaminase domain, CRISPR-associated adenosine deaminase 1 (Cad1). We show that upon binding of cA or cA to its CARF domain, Cad1 converts ATP to ITP, both in vivo and in vitro. Cryoelectron microscopy (cryo-EM) structural studies on full-length Cad1 reveal an hexameric assembly composed of a trimer of dimers, with bound ATP at inter-domain sites required for activity and ATP/ITP within deaminase active sites. Upon synthesis of cA during phage infection, Cad1 activation leads to a growth arrest of the host that prevents viral propagation. Our findings reveal that CRISPR-Cas systems employ a wide range of molecular mechanisms beyond nucleic acid degradation to provide adaptive immunity in prokaryotes.
History
DepositionJun 7, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45241.png

Downloads & links

-
Map

FileDownload / File: emd_45241.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationz-fliped main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0591
Minimum - Maximum-0.1341907 - 0.37145603
Average (Standard dev.)-0.0003789533 (±0.013214816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: halfmap-zflipped-half mapA

Fileemd_45241_half_map_1.map
Annotationhalfmap-zflipped-half mapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfmap-zflipped-half mapB

Fileemd_45241_half_map_2.map
Annotationhalfmap-zflipped-half mapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : apo Cad1 (CRISPR associated Adenosine deaminase 1) full length protein

EntireName: apo Cad1 (CRISPR associated Adenosine deaminase 1) full length protein
Components
  • Complex: apo Cad1 (CRISPR associated Adenosine deaminase 1) full length protein
    • Protein or peptide: Adenosine deaminase domain-containing protein
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: apo Cad1 (CRISPR associated Adenosine deaminase 1) full length protein

SupramoleculeName: apo Cad1 (CRISPR associated Adenosine deaminase 1) full length protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: It forms a trimer of dimers
Source (natural)Organism: Bacteriodale bacterium (bacteria)
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Adenosine deaminase domain-containing protein

MacromoleculeName: Adenosine deaminase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacteroidales bacterium (bacteria)
Molecular weightTheoretical: 67.264945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRVLLCSAG HSSMVVPEAF HAVPEGFEEV HVFTTDSEKF NPVVLNDFFH SLPNVRFSIT KCHGLADILN ERDFEFYQEM LWQWYLTKM PDNELPYVCL SGGIKSMSAS LQKAATLFGA QSVFHVLADN NPRNIEEMFD ALQKGQIHFI EMGYEPGWAA L RRLKKILP ...String:
MSRVLLCSAG HSSMVVPEAF HAVPEGFEEV HVFTTDSEKF NPVVLNDFFH SLPNVRFSIT KCHGLADILN ERDFEFYQEM LWQWYLTKM PDNELPYVCL SGGIKSMSAS LQKAATLFGA QSVFHVLADN NPRNIEEMFD ALQKGQIHFI EMGYEPGWAA L RRLKKILP INEGCSRDNF KPLISKSIEE ILSNVKIMAS DTGKSNQLPF PSLAILPPIA QQWLQLPLSA NDGAWIQNLP KV DLHCHLG GFATSGSLLD QVRGAASEPD LIDRTFSPQE IAGWPRSHKS ISLDKYMELG NANGSKLLKD KGCLIRQVEL LYQ SLVNDN VAYAEIRCSP NNYADKNKNR SAWVVLQDIN DTFTRLITEA KQKNQFYCHV NLLVIASRKF SGDLSDISKH LALA ITAMQ QGEGVCRIVG VDLAGFENKE TRASYYEHDF KAVHRCGLAV TAHAGENDDP EGIWQAVYSL HARRLGHALN LLEAP DLMR TVIERKIGVE MCPYANYQIK GFAPMPNFSA LYPLKKYLEA GILVSVNTDN IGISGANLSE NLLILADLCP GISRMD VLT IIRNSIETAF ISHDFRMELL KFFDRKIYDV CLISIKN

UniProtKB: adenosine deaminase

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.7 mg/mL
BufferpH: 8
Details: 25 mM Hepes pH 8, 200 mM NaCl, 2 mM Beta-mercaptoethanol and 5 % glycerol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
Details: Glow discharge 1 min, 15 mA 100 % humidity, wait time 12 s, 2.5 s blot time and 0 blot force at 4 degree C temperature
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 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: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
In silico model: The model was generated using alphaFold2. The initial map was generated by ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Half maps were generated by Non-uniform refinement programme using cryoSparc
Number images used: 110836
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9c67:
cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in apo form

+
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