[English] 日本語
Yorodumi
- EMDB-21366: Cryo-EM structure of AcrVIA1-Cas13(crRNA) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21366
TitleCryo-EM structure of AcrVIA1-Cas13(crRNA) complex
Map dataAcrVIA1-Cas13(crRNA) complex
Sample
  • Complex: Cas13-crRNA-AcrVIA1 complex
    • RNA: RNA (52-MER)
    • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
    • Protein or peptide: AcrVIA1
KeywordsCRISPR-Cas system / Cas13 / type VIA / IMMUNE SYSTEM / Anti-CRISPR / HYDROLASE / RNA
Function / homologyendonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesListeria seeligeri (bacteria) / Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria) / Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJia N / Meeske AJ
CitationJournal: Science / Year: 2020
Title: A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity.
Authors: Alexander J Meeske / Ning Jia / Alice K Cassel / Albina Kozlova / Jingqiu Liao / Martin Wiedmann / Dinshaw J Patel / Luciano A Marraffini /
Abstract: The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. ...The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. However, how viruses can counteract this immunity is not known. We describe a listeriaphage (ϕLS46) encoding an anti-CRISPR protein (AcrVIA1) that inactivates the type VI-A CRISPR system of Using genetics, biochemistry, and structural biology, we found that AcrVIA1 interacts with the guide-exposed face of Cas13a, preventing access to the target RNA and the conformational changes required for nuclease activation. Unlike inhibitors of DNA-cleaving Cas nucleases, which cause limited immunosuppression and require multiple infections to bypass CRISPR defenses, a single dose of AcrVIA1 delivered by an individual virion completely dismantles type VI-A CRISPR-mediated immunity.
History
DepositionFeb 7, 2020-
Header (metadata) releaseJun 10, 2020-
Map releaseJun 10, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vrb
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21366.png

Downloads & links

-
Map

FileDownload / File: emd_21366.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcrVIA1-Cas13(crRNA) complex
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.15897144 - 0.31338927
Average (Standard dev.)0.00029948552 (±0.0060298718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 211.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z211.680211.680211.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ180180180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.1590.3130.000

-
Supplemental data

-
Sample components

-
Entire : Cas13-crRNA-AcrVIA1 complex

EntireName: Cas13-crRNA-AcrVIA1 complex
Components
  • Complex: Cas13-crRNA-AcrVIA1 complex
    • RNA: RNA (52-MER)
    • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
    • Protein or peptide: AcrVIA1

-
Supramolecule #1: Cas13-crRNA-AcrVIA1 complex

SupramoleculeName: Cas13-crRNA-AcrVIA1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Listeria seeligeri (bacteria)

-
Macromolecule #1: RNA (52-MER)

MacromoleculeName: RNA (52-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Molecular weightTheoretical: 16.534871 KDa
SequenceString:
GACUACCUCU AUAUGAAAGA GGACUAAAAC CAUAUUUCCA AACUCCACUU UG

GENBANK: GENBANK: FN557490.1

-
Macromolecule #2: CRISPR-associated endoribonuclease Cas13a

MacromoleculeName: CRISPR-associated endoribonuclease Cas13a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954) (bacteria)
Strain: ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954
Molecular weightTheoretical: 128.350414 KDa
Recombinant expressionOrganism: Listeria seeligeri (bacteria)
SequenceString: TMRITKVEVD RKKVLISRDK NGGKLVYENE MQDNTEQIMH HKKSSFYKSV VNKTICRPEQ KQMKKLVHGL LQENSQEKIK VSDVTKLNI SNFLNHRFKK SLYYFPENSP DKSEEYRIEI NLSQLLEDSL KKQQGTFICW ESFSKDMELY INWAENYISS K TKLIKKSI ...String:
TMRITKVEVD RKKVLISRDK NGGKLVYENE MQDNTEQIMH HKKSSFYKSV VNKTICRPEQ KQMKKLVHGL LQENSQEKIK VSDVTKLNI SNFLNHRFKK SLYYFPENSP DKSEEYRIEI NLSQLLEDSL KKQQGTFICW ESFSKDMELY INWAENYISS K TKLIKKSI RNNRIQSTES RSGQLMDRYM KDILNKNKPF DIQSVSEKYQ LEKLTSALKA TFKEAKKNDK EINYKLKSTL QN HERQIIE ELKENSELNQ FNIEIRKHLE TYFPIKKTNR KVGDIRNLEI GEIQKIVNHR LKNKIVQRIL QEGKLASYEI EST VNSNSL QKIKIEEAFA LKFINACLFA SNNLRNMVYP VCKKDILMIG EFKNSFKEIK HKKFIRQWSQ FFSQEITVDD IELA SWGLR GAIAPIRNEI IHLKKHSWKK FFNNPTFKVK KSKIINGKTK DVTSEFLYKE TLFKDYFYSE LDSVPELIIN KMESS KILD YYSSDQLNQV FTIPNFELSL LTSAVPFAPS FKRVYLKGFD YQNQDEAQPD YNLKLNIYNE KAFNSEAFQA QYSLFK MVY YQVFLPQFTT NNDLFKSSVD FILTLNKERK GYAKAFQDIR KMNKDEKPSE YMSYIQSQLM LYQKKQEEKE KINHFEK FI NQVFIKGFNS FIEKNRLTYI CHPTKNTVPE NDNIEIPFHT DMDDSNIAFW LMCKLLDAKQ LSELRNEMIK FSCSLQST E EISTFTKARE VIGLALLNGE KGCNDWKELF DDKEAWKKNM SLYVSEELLQ SLPYTQEDGQ TPVINRSIDL VKKYGTETI LEKLFSSSDD YKVSAKDIAK LHEYDVTEKI AQQESLHKQW IEKPGLARDS AWTKKYQNVI NDISNYQWAK TKVELTQVRH LHQLTIDLL SRLAGYMSIA DRDFQFSSNY ILERENSEYR VTSWILLSEN KNKNKYNDYE LYNLKNASIK VSSKNDPQLK V DLKQLRLT LEYLELFDNR LKEKRNNISH FNYLNGQLGN SILELFDDAR DVLSYDRKLK NAVSKSLKEI LSSHGMEVTF KP LYQTNHH LKIDKLQPKK IHHLGEKSTV SSNQVSNEYC QLVRTLLTMK

UniProtKB: CRISPR-associated endoribonuclease Cas13a

-
Macromolecule #3: AcrVIA1

MacromoleculeName: AcrVIA1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria seeligeri (bacteria)
Molecular weightTheoretical: 27.144854 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIYYIKDLKV KGKIFENLMN KEAVEGLITF LKKAEFEIYS RENYSKYNKW FEMWKSPTSS LVFWKNYSFR CHLLFVIEKD GECLGIPAS VFESVLQIYL ADPFAPDTKE LFVEVCNLYE CLADVTVVEH FEAEESAWHK LTHNETEVSK RVYSKDDDEL L KYIPEFLD ...String:
MIYYIKDLKV KGKIFENLMN KEAVEGLITF LKKAEFEIYS RENYSKYNKW FEMWKSPTSS LVFWKNYSFR CHLLFVIEKD GECLGIPAS VFESVLQIYL ADPFAPDTKE LFVEVCNLYE CLADVTVVEH FEAEESAWHK LTHNETEVSK RVYSKDDDEL L KYIPEFLD TIATNKKSQK YNQIQGKIQE INKEIATLYE SSEDYIFTEY VSNLYRESAK LEQHSKQILK E

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.23 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 717725
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