[English] 日本語
Yorodumi
- EMDB-35926: Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35926
TitleCryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA
Map data
Sample
  • Complex: AsCas12f-YHAM-sgRNAS3-5v7-target DNA
    • Protein or peptide: Transposase IS605 OrfB C-terminal domain-containing protein
    • DNA: DNA (38-MER)
    • DNA: DNA (38-MER)
    • RNA: RNA (118-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsCRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex
Function / homologyTransposase IS605, OrfB, C-terminal / Putative transposase DNA-binding domain / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding / CRISPR-associated endodeoxyribonuclease Cas12f1
Function and homology information
Biological speciesSulfoacidibacillus thermotolerans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsHino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H ...Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / Itoh Y / Matoba S / Aburatani H / Yachie N / Siksnys V / Ohmori T / Hoshino A / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Minimal and most efficient genome editing Cas enzyme
Authors: Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / ...Authors: Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / Itoh Y / Matoba S / Aburatani H / Yachie N / Siksnys V / Ohmori T / Hoshino A / Nureki O
History
DepositionApr 13, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35926.png

Downloads & links

-
Map

FileDownload / File: emd_35926.map.gz / Format: CCP4 / Size: 4.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.328 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.004871192 - 2.1486135
Average (Standard dev.)0.010326324 (±0.077385545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin464646
Dimensions108108108
Spacing108108108
CellA=B=C: 143.424 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35926_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35926_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AsCas12f-YHAM-sgRNAS3-5v7-target DNA

EntireName: AsCas12f-YHAM-sgRNAS3-5v7-target DNA
Components
  • Complex: AsCas12f-YHAM-sgRNAS3-5v7-target DNA
    • Protein or peptide: Transposase IS605 OrfB C-terminal domain-containing protein
    • DNA: DNA (38-MER)
    • DNA: DNA (38-MER)
    • RNA: RNA (118-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: AsCas12f-YHAM-sgRNAS3-5v7-target DNA

SupramoleculeName: AsCas12f-YHAM-sgRNAS3-5v7-target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Sulfoacidibacillus thermotolerans (bacteria)

-
Macromolecule #1: Transposase IS605 OrfB C-terminal domain-containing protein

MacromoleculeName: Transposase IS605 OrfB C-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sulfoacidibacillus thermotolerans (bacteria)
Molecular weightTheoretical: 49.966105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGS MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGYSS DYKDNHGEYP KSKDILGYTN VHGYAYHTI KTKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL S NPAKQEMN ...String:
MGHHHHHHGS MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGYSS DYKDNHGEYP KSKDILGYTN VHGYAYHTI KTKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL S NPAKQEMN VKRKISVIII VRGAGKTIMD RILSGEYQVH ASQIIHDDRK NKWYLNISYD FEPQTRVLDL NKIMGIDLGV AV AAYMAFQ HTPARYKLEG GEIENFRRQV ESRRISMLRQ GKYAGGARGG HGRDKRIKPI EQLRDKIANF RDTTNHRYSR YIV DMAIKM GCGTIQMEDL TNIRDIGSRF LQNWTYYDLQ QKIIYKAEEA GIKVIKIDPQ YTSQRCSECG NIDSGNRIGQ AIFK CRACG YEANADYNAA RNIAIPNIDK IIAESIK

UniProtKB: CRISPR-associated endodeoxyribonuclease Cas12f1

-
Macromolecule #2: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Sulfoacidibacillus thermotolerans (bacteria)
Molecular weightTheoretical: 11.694576 KDa
SequenceString:
(DG)(DA)(DA)(DT)(DG)(DG)(DT)(DT)(DC)(DA) (DA)(DG)(DC)(DG)(DC)(DA)(DC)(DC)(DT)(DA) (DA)(DT)(DT)(DT)(DC)(DC)(DT)(DA)(DA) (DA)(DT)(DT)(DA)(DG)(DA)(DA)(DA)(DA)

-
Macromolecule #3: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Sulfoacidibacillus thermotolerans (bacteria)
Molecular weightTheoretical: 11.689535 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DT) (DT)(DA)(DG)(DG)(DA)(DA)(DA)(DT)(DT)(DA) (DG)(DG)(DT)(DG)(DC)(DG)(DC)(DT)(DT) (DG)(DA)(DA)(DC)(DC)(DA)(DT)(DT)(DC)

-
Macromolecule #4: RNA (118-MER)

MacromoleculeName: RNA (118-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Sulfoacidibacillus thermotolerans (bacteria)
Molecular weightTheoretical: 38.288805 KDa
SequenceString:
GGAUUCGUCG GUUCAGCGAC GAUAAGCCGA GAAGUGCCAA UAAAACUGUU AAGUGGUUUG GUAACGCUCG GUAAGGUCCG AAAGGAGAA CCACUGAACG GAAAUUAGGU GCGCUUGGC

-
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / 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: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146448
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