[English] 日本語
Yorodumi
- EMDB-6777: Electron cryo-microscopy structure of LbuCas13a-crRNA binary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6777
TitleElectron cryo-microscopy structure of LbuCas13a-crRNA binary complex
Map dataElectron cryo-microscopy structure of LbuCas13a-crRNA binary complex
Sample
  • Complex: LbuCas13a-crRNA binary complex
    • Protein or peptide: A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a
    • RNA: RNA (59-MER)
KeywordsCas13a / CRISPR / RNA BINDING PROTEIN-RNA COMPLEX
Function / homologydefense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesLeptotrichia buccalis (bacteria) / Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang X / Wang Y
Funding support China, 3 items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2014CB910102 China
the Natural Science Foundation of China91440201, 31571335, 31400640, 31570874 China
the Strategic Priority Research Program of the Chinese Academy of SciencesXDB08010203 China
CitationJournal: Cell / Year: 2017
Title: The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a.
Authors: Liang Liu / Xueyan Li / Jun Ma / Zongqiang Li / Lilan You / Jiuyu Wang / Min Wang / Xinzheng Zhang / Yanli Wang /
Abstract: Cas13a, a type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, degrades invasive RNAs targeted by CRISPR RNA (crRNA) and has potential applications in RNA technology. To understand how Cas13a ...Cas13a, a type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, degrades invasive RNAs targeted by CRISPR RNA (crRNA) and has potential applications in RNA technology. To understand how Cas13a is activated to cleave RNA, we have determined the crystal structure of Leptotrichia buccalis (Lbu) Cas13a bound to crRNA and its target RNA, as well as the cryo-EM structure of the LbuCas13a-crRNA complex. The crRNA-target RNA duplex binds in a positively charged central channel of the nuclease (NUC) lobe, and Cas13a protein and crRNA undergo a significant conformational change upon target RNA binding. The guide-target RNA duplex formation triggers HEPN1 domain to move toward HEPN2 domain, activating the HEPN catalytic site of Cas13a protein, which subsequently cleaves both single-stranded target and collateral RNAs in a non-specific manner. These findings reveal how Cas13a of type VI CRISPR-Cas systems defend against RNA phages and set the stage for its development as a tool for RNA manipulation.
History
DepositionJun 30, 2017-
Header (metadata) releaseSep 13, 2017-
Map releaseSep 13, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / 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-5xwy
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6777.png

Downloads & links

-
Map

FileDownload / File: emd_6777.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron cryo-microscopy structure of LbuCas13a-crRNA binary complex
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.12865293 - 0.20330638
Average (Standard dev.)0.00039493514 (±0.0066677476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 164.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z164.000164.000164.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1290.2030.000

-
Supplemental data

-
Sample components

-
Entire : LbuCas13a-crRNA binary complex

EntireName: LbuCas13a-crRNA binary complex
Components
  • Complex: LbuCas13a-crRNA binary complex
    • Protein or peptide: A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a
    • RNA: RNA (59-MER)

-
Supramolecule #1: LbuCas13a-crRNA binary complex

SupramoleculeName: LbuCas13a-crRNA binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leptotrichia buccalis (bacteria) / Strain: ATCC 14201

-
Macromolecule #1: A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a

MacromoleculeName: A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b) (bacteria)
Strain: ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b
Molecular weightTheoretical: 138.555156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKVTKVGGIS HKKYTSEGRL VKSESEENRT DERLSALLNM RLDMYIKNPS STETKENQKR IGKLKKFFSN KMVYLKDNTL SLKNGKKEN IDREYSETDI LESDVRDKKN FAVLKKIYLN ENVNSEELEV FRNDIKKKLN KINSLKYSFE KNKANYQKIN E NNIEKVEG ...String:
MKVTKVGGIS HKKYTSEGRL VKSESEENRT DERLSALLNM RLDMYIKNPS STETKENQKR IGKLKKFFSN KMVYLKDNTL SLKNGKKEN IDREYSETDI LESDVRDKKN FAVLKKIYLN ENVNSEELEV FRNDIKKKLN KINSLKYSFE KNKANYQKIN E NNIEKVEG KSKRNIIYDY YRESAKRDAY VSNVKEAFDK LYKEEDIAKL VLEIENLTKL EKYKIREFYH EIIGRKNDKE NF AKIIYEE IQNVNNMKEL IEKVPDMSEL KKSQVFYKYY LDKEELNDKN IKYAFCHFVE IEMSQLLKNY VYKRLSNISN DKI KRIFEY QNLKKLIENK LLNKLDTYVR NCGKYNYYLQ DGEIATSDFI ARNRQNEAFL RNIIGVSSVA YFSLRNILET ENEN DITGR MRGKTVKNNK GEEKYVSGEV DKIYNENKKN EVKENLKMFY SYDFNMDNKN EIEDFFANID EAISSIRHGI VHFNL ELEG KDIFAFKNIA PSEISKKMFQ NEINEKKLKL KIFRQLNSAN VFRYLEKYKI LNYLKRTRFE FVNKNIPFVP SFTKLY SRI DDLKNSLGIY WKTPKTNDDN KTKEIIDAQI YLLKNIYYGE FLNYFMSNNG NFFEISKEII ELNKNDKRNL KTGFYKL QK FEDIQEKIPK EYLANIQSLY MINAGNQDEE EKDTYIDFIQ KIFLKGFMTY LANNGRLSLI YIGSDEETNT SLAEKKQE F DKFLKKYEQN NNIKIPYEIN EFLREIKLGN ILKYTERLNM FYLILKLLNH KELTNLKGSL EKYQSANKEE AFSDQLELI NLLNLDNNRV TEDFELEADE IGKFLDFNGN KVKDNKELKK FDTNKIYFDG ENIIKHRAFY NIKKYGMLNL LEKIADKAGY KISIEELKK YSNKKNEIEK NHKMQENLHR KYARPRKDEK FTDEDYESYK QAIENIEEYT HLKNKVEFNE LNLLQGLLLR I LHRLVGYT SIWERDLRFR LKGEFPENQY IEEIFNFENK KNVKYKGGQI VEKYIKFYKE LHQNDEVKIN KYSSANIKVL KQ EKKDLYI ANYIAAFNYI PHAEISLLEV LENLRKLLSY DRKLKNAVMK SVVDILKEYG FVATFKIGAD KKIGIQTLES EKI VHLKNL KKKKLMTDRN SEELCKLVKI MFEYKMEEKK SEN

UniProtKB: CRISPR-associated endoribonuclease Cas13a

-
Macromolecule #2: RNA (59-MER)

MacromoleculeName: RNA (59-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.869348 KDa
SequenceString:
GGACCACCCC AAAAAUGAAG GGGACUAAAA CACAAAUCUA UCUGAAUAAA CUCUUCUUC

-
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 K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238758

+
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