[English] 日本語
Yorodumi
- EMDB-52286: Structure of cleaved tRNA fragment bound Ba1Cas12a3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52286
TitleStructure of cleaved tRNA fragment bound Ba1Cas12a3
Map data
Sample
  • Complex: Postcleavage tRNA fragment bound Ba1Cas12a3
    • Protein or peptide: Ba1Cas12a3
    • RNA: crRNA
    • RNA: target RNA
    • RNA: Cleaved 3' tRNA fragment
  • Ligand: MAGNESIUM ION
Keywordscrispar-cas nuclease / RNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesBacteroidota bacterium (bacteria) / synthetic construct (others) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYuan B / Heinz DW
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of cleaved tRNA fragment bound Ba1Cas12a3
Authors: Yuan B / Heinz DW
History
DepositionDec 6, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52286.png

Downloads & links

-
Map

FileDownload / File: emd_52286.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.11138095 - 0.19374812
Average (Standard dev.)0.000031774092 (±0.0035208645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_52286_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52286_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Postcleavage tRNA fragment bound Ba1Cas12a3

EntireName: Postcleavage tRNA fragment bound Ba1Cas12a3
Components
  • Complex: Postcleavage tRNA fragment bound Ba1Cas12a3
    • Protein or peptide: Ba1Cas12a3
    • RNA: crRNA
    • RNA: target RNA
    • RNA: Cleaved 3' tRNA fragment
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Postcleavage tRNA fragment bound Ba1Cas12a3

SupramoleculeName: Postcleavage tRNA fragment bound Ba1Cas12a3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Bacteroidota bacterium (bacteria)

-
Macromolecule #1: Ba1Cas12a3

MacromoleculeName: Ba1Cas12a3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroidota bacterium (bacteria)
Molecular weightTheoretical: 135.303656 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: METYKVTKTI RFKLEAQNVP EIQKDIEGLQ SEFNLANFVS DLKNYLDQVR NYLFSEGKEH VFVNNKITIK REWLQNHAKQ EWVDFLEKN KRNNSLNNHT RRIQMSIGDF TGLASKIEGT FDEINSICKG LADAAGAQAN KRTKRERTGL LLKRLQARKA L PSLFSLIE ...String:
METYKVTKTI RFKLEAQNVP EIQKDIEGLQ SEFNLANFVS DLKNYLDQVR NYLFSEGKEH VFVNNKITIK REWLQNHAKQ EWVDFLEKN KRNNSLNNHT RRIQMSIGDF TGLASKIEGT FDEINSICKG LADAAGAQAN KRTKRERTGL LLKRLQARKA L PSLFSLIE NSADKNETGN LSLQLKNKSI LIEQQLAAGV QTFLPAQSGG LPVAKASFNY YTINKKPVDF GNEKSELESR LK ISIDTIF KLTRENFSKK IEEAITADIQ KELNNGKTLL LGDVPMLGIE NYVSLRQILK NIKSNQKKAF SDLMQSGKNY NEL KATNLY LLNTIEQRQF DNYKVKTNEL EKLAVKINQA TNDNQKKELI SNKQRVAKQR GIIMRDNFAT WKSFSNFYRT ISQE HGKIL ALLKGIEKER TESQLLKYWA LILENNGQHK LILIPREKAA SCKQWIASLN PSGDKLTKLF WFESLTYRSL QKLCF GFTE NGNNKFNKNI QNLLPKDNSR KIINGEFAFQ GDEQKKIKFY QSVLESKYAQ SVLNIPIQQV QADIINQSFA SLDDFQ IAL EKICYRLFAV VEANIEAELL KNDKAQIFNI TSSDLRKEAK DKIKSHTQIW KAFWTSENKQ NNFETRLNPE ITITYRQ PK QSKIDKYGER SQKNNRYLHA QYTLITTISE HSNSPTKILS FMSDDEFKSS VDTFNKKFKK DEIKFAFGID NGEVELST L GVYFPAFDKT TYKEKVAELE KVNDYGFEVL TIRNLNYKET DYNGKERKII QNPSYFLKKE NYLRTFNKSE TAYQKMFTE QFEKKKLLTL DLTTAKVICG HIVTNGDVPA LFNLWLKHAQ RNIFEMNDHI QKETAKKIVL KNQLDTDNEK LKFAEYISKE KEFGKLNDD EKMKYTKWIF EDRDQNNFTE VENKKFKRCQ KIYGNYSTKA KAPVLFASCF IDEELQSVTD IFDVRHIFKK R EDFYALKT EEEIKQLIDS YNTNRASHDI SNEELDLKIL NTKKALVANA VGVIDFLYKH YERRLGGEGL IIKEGFGTGK VE DGIEKFS GNIYRILERK LYQKFQNYGL VPPIKSLMAV RANGIENNKN AILQLGNVGF IDPAGTSQEC PVCIEGRLEH TTT CPNKCG FNSERIMHSN DGIASFNIAK RGFNNFVKSK TDKQLEHHHH HH

UniProtKB: UNIPROTKB: A0A2N2ZXC5

-
Macromolecule #2: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.859344 KDa
SequenceString:
GUCUAAACCG ACCCAAUAAU UUCUACUGUU GUAGAUGAGG GAUCUCGCUC CUGGAAGAUG GUGAU

-
Macromolecule #3: target RNA

MacromoleculeName: target RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.292981 KDa
SequenceString:
AAUCCCAUCA CCAUCUUCCA GGAGCGAGAU CCCUCCAAAA UC

-
Macromolecule #4: Cleaved 3' tRNA fragment

MacromoleculeName: Cleaved 3' tRNA fragment / type: rna / ID: 4 / Details: Ala tRNA / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.476531 KDa
SequenceString:
GGGGCUAUAG CUCAGCUGGG AGAGCGCCUG CUUUGCACGC AGGAGGUCUG CGGUUCGAUC CCGCAUAGCU CCACCA

GENBANK: GENBANK: CP053605.1

-
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

Concentration1.2 mg/mL
BufferpH: 7.5 / Details: 50mM TrisHCl 50mM NaCl 1mM DTT pH7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45337
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