[English] 日本語
Yorodumi
- EMDB-62001: Cryo-EM structure of the HfmIscB-omega RNA-target DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62001
TitleCryo-EM structure of the HfmIscB-omega RNA-target DNA complex
Map data
Sample
  • Complex: Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex
    • Protein or peptide: HfmIscB
    • RNA: Omega RNA
    • DNA: Target DNA strand
    • DNA: Non-target DNA strand
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRNA-guided DNA nuclease / RNA BINDING PROTEIN
Biological speciesmetagenome (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsNagahata N / Yamada S / Yamashita K / Nishimasu H
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05281 Japan
Japan Society for the Promotion of Science (JSPS)JP22H00403 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex
Authors: Nagahata N
History
DepositionOct 18, 2024-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62001.png

Downloads & links

-
Map

FileDownload / File: emd_62001.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 288 pix.
= 298.8 Å		1.04 Å/pix.
x 288 pix.
= 298.8 Å		1.04 Å/pix.
x 288 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.3383789 - 3.6397984
Average (Standard dev.)-0.0066023516 (±0.063411005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 298.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62001_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62001_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62001_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex

EntireName: Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex
Components
  • Complex: Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex
    • Protein or peptide: HfmIscB
    • RNA: Omega RNA
    • DNA: Target DNA strand
    • DNA: Non-target DNA strand
  • Ligand: MAGNESIUM ION
  • Ligand: water

-
Supramolecule #1: Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex

SupramoleculeName: Cryo-EM structure of the OavvIscB-omega RNA-target DNA complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: metagenome (others)

-
Macromolecule #1: HfmIscB

MacromoleculeName: HfmIscB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 62.381379 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADLSKHHHH SGHHHTGHHH HSGSHHHTGS AAGGEEDKKP AGGEGGGAHI NLKVKGQDGN EVFFRIKRST QLKKLMNAYC DRQSVDMTA IAFLFDGRRL RAEQTPDELE MEDGDEIDAM LHQTGGSSGS MAYCFVVDKN NRPLAPTKVN KGWYLVRKGR A KIKSRYPM ...String:
MADLSKHHHH SGHHHTGHHH HSGSHHHTGS AAGGEEDKKP AGGEGGGAHI NLKVKGQDGN EVFFRIKRST QLKKLMNAYC DRQSVDMTA IAFLFDGRRL RAEQTPDELE MEDGDEIDAM LHQTGGSSGS MAYCFVVDKN NRPLAPTKVN KGWYLVRKGR A KIKSRYPM VIQLEKEVEP DKYDESRVVV GIDDGSAHVG LAIVQKCPTK NKVVFKGTIE QRQDVKHLMD VRRGYRRYHR YH KRYRQAR FNNRHSSKRS GRLAPSIKQK KDAVLRVLYQ LNRWINIQEY YLEDVCMDIR AMTDGYKPYR WQYQKSSRLD ENL RKAAII RDGCKCQECG RSNCVLEVAH IKARKYGGAD TIGNLITLCS GCHQKTEGRE REFEDRYFKI IGSKPKRFDY AMHV MQGKN YLRERISELG PLHLTNGGET ANKRIEWNIV KSHSNDAICI TDCISDTCDV KEWIIKPMRR KSKAKTDNVL GIRHR DLVS YTYKNGEIHT GYVTALYPEL LALNFQSKTK HCKKVNAQKC RLLWKFDKIY WLEQCV

-
Macromolecule #2: Omega RNA

MacromoleculeName: Omega RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 115.337195 KDa
SequenceString: GGAAUUGUGA GCGGAUAACA AUUCCCCAGG ACUAAUUAUU AAGCAGUCUA AUAUAUAGAC AAAAGUGUAA ACAAGUGGAC AAGUGUAUA AUUACAUUUC UUGUUUACAC UUGCUUAACA AUAGGUUUCA AGCCUUAGUG ACUGCUACUA UCGAAAGAUA U GUUGCAGA ...String:
GGAAUUGUGA GCGGAUAACA AUUCCCCAGG ACUAAUUAUU AAGCAGUCUA AUAUAUAGAC AAAAGUGUAA ACAAGUGGAC AAGUGUAUA AUUACAUUUC UUGUUUACAC UUGCUUAACA AUAGGUUUCA AGCCUUAGUG ACUGCUACUA UCGAAAGAUA U GUUGCAGA UACGAACUAC GUUAGGGAAA AGGUUAAAGA CACACCUUUA GAUGUACUCG UCAGUCUGAA GCUCUGUGAG UG CCAAUCA AGAAACUGUG CUAAUGUCCU GUACAGAUAA CAGAGAAACA CAUAUACCUU CCCCGACAUU GGCAAGACGA AGA UUACUC CGAAAGGAAG GUAUCCAGAG AUGGAAAAUG AA

-
Macromolecule #3: Target DNA strand

MacromoleculeName: Target DNA strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.047669 KDa
SequenceString:
(DG)(DA)(DA)(DT)(DG)(DG)(DT)(DT)(DC)(DC) (DT)(DC)(DC)(DC)(DG)(DG)(DG)(DG)(DA)(DA) (DT)(DT)(DG)(DT)(DT)(DA)(DT)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DT) (DC) (DC)(DT)(DT)(DA)(DG)(DA)(DA)(DA) (DA)

-
Macromolecule #4: Non-target DNA strand

MacromoleculeName: Non-target DNA strand / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.329829 KDa
SequenceString:
(DG)(DG)(DG)(DA)(DG)(DG)(DA)(DA)(DC)(DC) (DA)(DT)(DT)(DC)

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 17 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 689275
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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