[English] 日本語
Yorodumi
- EMDB-39750: The structure of type III CRISPR-associated deaminase in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39750
TitleThe structure of type III CRISPR-associated deaminase in complex cA6 and ATP, fully activated
Map data
Sample
  • Complex: CAAD:CA6:ATP 6:3:6
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
    • Protein or peptide: Adenosine deaminase domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordsdefense system / deaminase / IMMUNE SYSTEM
Function / homologyinosine biosynthetic process / Adenosine deaminase domain / Adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / Adenosine/adenine deaminase / Metal-dependent hydrolase / Adenosine deaminase domain-containing protein
Function and homology information
Biological speciesLimisphaera ngatamarikiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen MR / Li ZX / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: Antiviral signaling of a type III CRISPR-associated deaminase.
Authors: Yutao Li / Zhaoxing Li / Purui Yan / Chenyang Hua / Jianping Kong / Wanqian Wu / Yurong Cui / Yan Duan / Shunxiang Li / Guanglei Li / Shunli Ji / Yijun Chen / Yucheng Zhao / Peng Yang / ...Authors: Yutao Li / Zhaoxing Li / Purui Yan / Chenyang Hua / Jianping Kong / Wanqian Wu / Yurong Cui / Yan Duan / Shunxiang Li / Guanglei Li / Shunli Ji / Yijun Chen / Yucheng Zhao / Peng Yang / Chunyi Hu / Meiling Lu / Meirong Chen / Yibei Xiao /
Abstract: Prokaryotes have evolved diverse defense strategies against viral infection, such as foreign nucleic acid degradation by CRISPR-Cas systems and DNA/RNA synthesis inhibition via nucleotide pool ...Prokaryotes have evolved diverse defense strategies against viral infection, such as foreign nucleic acid degradation by CRISPR-Cas systems and DNA/RNA synthesis inhibition via nucleotide pool depletion. Here, we report an antiviral mechanism of type III CRISPR-Cas-regulated ATP depletion, where ATP is converted into ITP by CRISPR-Cas-associated adenosine deaminase (CAAD) upon activation by either cA or cA, followed by hydrolysis into IMP by Nudix hydrolase, ultimately resulting in cell growth arrest. The cryo-electron microscopy structures of CAAD in its apo and activated forms, together with biochemical evidence, revealed how cA/cA binds to the CARF domain and abrogates CAAD autoinhibition, inducing substantial conformational changes that reshape the structure of CAAD and induce its deaminase activity. Our results reveal the mechanism of a CRISPR-Cas-regulated ATP depletion antiviral strategy.
History
DepositionApr 15, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39750.png

Downloads & links

-
Map

FileDownload / File: emd_39750.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 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-0.024852645 - 0.68628323
Average (Standard dev.)0.0053423047 (±0.015413953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 477.184 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_39750_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39750_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39750_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CAAD:CA6:ATP 6:3:6

EntireName: CAAD:CA6:ATP 6:3:6
Components
  • Complex: CAAD:CA6:ATP 6:3:6
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
    • Protein or peptide: Adenosine deaminase domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: CAAD:CA6:ATP 6:3:6

SupramoleculeName: CAAD:CA6:ATP 6:3:6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)

-
Macromolecule #1: 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: 1 / Number of copies: 3
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

-
Macromolecule #2: Adenosine deaminase domain-containing protein

MacromoleculeName: Adenosine deaminase domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Molecular weightTheoretical: 69.899766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NVQAHLFVSL GTAPAIVPEA FLLPGARFVS VHVLTTERPD VTLIREFFRR HAPGVNLTIT RVAGFQDLKS EEDHFRFEEV MFRWFLASR TGPEQRFVCL TGGFKTMSAA MQKAATVLGA AEVFHVLADD CCVGPQGRLM PPSTLEEILW ARDQGHLHWI R LGPERGWP ...String:
NVQAHLFVSL GTAPAIVPEA FLLPGARFVS VHVLTTERPD VTLIREFFRR HAPGVNLTIT RVAGFQDLKS EEDHFRFEEV MFRWFLASR TGPEQRFVCL TGGFKTMSAA MQKAATVLGA AEVFHVLADD CCVGPQGRLM PPSTLEEILW ARDQGHLHWI R LGPERGWP QLRRIAPEQF PLQVVEEKGD ERRVQAEDRA FGTFLQDLLQ RASRIAGAWE MLPELPFADL ATWSEGELAW LR EPLDPRA PADQRWVAGL PKIELHCHLG GFATHGELLR RVRNAAENPG KLPPLEEPRL PEGWPLPAQP IPLAEYMKLG NAN GTALLR DPGCLREQCR LLYRHLVDQG VCYAEVRCSP ANYAEVRSPW DVLADIRAAF QECMEGARTA PGGLPACHVN LILI ATRRA SGDYRAAIAR HLALAVTAAE HWRDENACRV VGVDLAGYED EKTRAHYFRE EFTAVHRCGL AVTVHAGEND DAEGI WRAV FDLNARRLGH ALSLGQSREL LRSVADRGIG VELCPYANLQ IKGFRLDGSD RAGPADPRHE AHAPGPYPLL DYLREG VRV TVNTDNIGIS AASLTDNLLL AARLCPGLTR LDLLHLQRHA LETAFCTATQ RLTLLRRISS GIPRP

UniProtKB: Adenosine deaminase domain-containing protein

-
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

-
Macromolecule #4: ZINC ION

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

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55742
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: RANDOM ASSIGNMENT

+
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