[English] 日本語
Yorodumi
- EMDB-48630: Cryo-EM structure of CRISPR-associated cA4 bound Cat1 Pentagonal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48630
TitleCryo-EM structure of CRISPR-associated cA4 bound Cat1 Pentagonal filament assembly in the presence of NAD (ADPR modelled)
Map dataMain cryo-EM map Z-flipped
Sample
  • Complex: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex NAD substrate was mixed with the sample.
    • Protein or peptide: Cat1 (CRISPR associated TIR 1) pentagonal filament assembly
    • RNA: RNA (5'-R(P*AP*AP*AP*A)-3')
  • Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
KeywordsCRISPR / antiphage defense / adaptive immunity / Filament / CARF / TIR / NAD / ADPR / NAM / ANTIVIRAL PROTEIN
Biological speciesbacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMajumder P / Patel DJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM129430 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM145888 United States
CitationJournal: Science / Year: 2025
Title: Cat1 forms filament networks to degrade NAD during the type III CRISPR-Cas antiviral response.
Authors: Christian F Baca / Puja Majumder / James H Hickling / Dinshaw J Patel / Luciano A Marraffini /
Abstract: Type III CRISPR-Cas systems defend against viral infection in prokaryotes by using an RNA-guided complex that recognizes foreign transcripts and synthesizes cyclic oligoadenylate (cOA) messengers to ...Type III CRISPR-Cas systems defend against viral infection in prokaryotes by using an RNA-guided complex that recognizes foreign transcripts and synthesizes cyclic oligoadenylate (cOA) messengers to activate CRISPR-associated Rossmann-fold (CARF) immune effectors. In this study, we investigated a protein containing a CARF domain-fused Toll/interleukin-1 receptor (TIR) domain, Cat1. We found that Cat1 provides immunity by cleaving and depleting oxidized nicotinamide adenine dinucleotide (NAD) molecules from the infected host, inducing a growth arrest that prevents viral propagation. Cat1 forms dimers that stack upon each other to generate long filaments that are maintained by bound cOA ligands, with stacked TIR domains forming the NAD cleavage catalytic sites. Furthermore, Cat1 filaments assemble into distinct trigonal and pentagonal networks that enhance NAD degradation. Cat1 presents an unprecedented chemistry and higher-order protein assembly for the CRISPR-Cas response.
History
DepositionJan 13, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48630.png

Downloads & links

-
Map

FileDownload / File: emd_48630.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain cryo-EM map Z-flipped
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 438.272 Å		0.86 Å/pix.
x 512 pix.
= 438.272 Å		0.86 Å/pix.
x 512 pix.
= 438.272 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: 0.13
Minimum - Maximum-0.7297133 - 1.1902366
Average (Standard dev.)0.005066168 (±0.050016254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 438.272 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: cryo-EM map half map A Z-flipped

Fileemd_48630_half_map_1.map
Annotationcryo-EM map half map A Z-flipped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: cryo-EM map half map B Z-flipped

Fileemd_48630_half_map_2.map
Annotationcryo-EM map half map B Z-flipped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex NAD subst...

EntireName: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex NAD substrate was mixed with the sample.
Components
  • Complex: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex NAD substrate was mixed with the sample.
    • Protein or peptide: Cat1 (CRISPR associated TIR 1) pentagonal filament assembly
    • RNA: RNA (5'-R(P*AP*AP*AP*A)-3')
  • Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE

-
Supramolecule #1: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex NAD subst...

SupramoleculeName: Antiviral protein Cat1 - Cyclic Tetra-Adenylate Complex NAD substrate was mixed with the sample.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Cat1 protein forms filament structure upon recognition of cA4, Cyclic Tetra-Adenylate ligand. NAD substrate was mixed with the sample.
Source (natural)Organism: bacterium (bacteria)

-
Macromolecule #1: Cat1 (CRISPR associated TIR 1) pentagonal filament assembly

MacromoleculeName: Cat1 (CRISPR associated TIR 1) pentagonal filament assembly
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 30.150592 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPQAFFSHNN KDKKIVLEVL EHLRQSLVAT WIDQQSIPGG GSLIQQIIAG ISKSQYFLAF LSNEYLKSDW CWDELEQAYA LHQKGKVKI IPILLTNRAQ LDLNALTDAR RNFLESILTR LKYVEFDPHN MTRSLGSVAE ALWQNEAVRF EPIRMIKVNG T ELQVVEFK ...String:
MPQAFFSHNN KDKKIVLEVL EHLRQSLVAT WIDQQSIPGG GSLIQQIIAG ISKSQYFLAF LSNEYLKSDW CWDELEQAYA LHQKGKVKI IPILLTNRAQ LDLNALTDAR RNFLESILTR LKYVEFDPHN MTRSLGSVAE ALWQNEAVRF EPIRMIKVNG T ELQVVEFK IPGSNLPVDF LHHWDLKIED FIATSPNEQK PVKFDVPVAL YGPGPNWLYA FLTLPFKNRN TVFVFNSRTS EY ICVYSKS AGLAPGMVLK GHHHHH

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

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 1.271866 KDa
SequenceString:
AAAA

-
Macromolecule #3: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]ME...

MacromoleculeName: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
type: ligand / ID: 3 / Number of copies: 2 / Formula: AR6
Molecular weightTheoretical: 559.316 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: liquid-nitrogen-cooled liquid ethane was used as the cryogen..

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.32 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: 2.0 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: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152750
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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