[English] 日本語
Yorodumi
- EMDB-62609: Cryo-EM structure of Leptospirillum ferriphilum helicase Dda -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62609
TitleCryo-EM structure of Leptospirillum ferriphilum helicase Dda
Map data
Sample
  • Complex: LfDda
    • Protein or peptide: Putative deoxyribonuclease
KeywordsHelicases / nanopore sequencing / Leptospirillum ferriphilum / DNA BINDING PROTEIN
Function / homologyUvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / AAA domain / DNA helicase activity / : / P-loop containing nucleoside triphosphate hydrolase / Putative deoxyribonuclease
Function and homology information
Biological speciesLeptospirillum ferriphilum (strain ML-04) (bacteria) / Leptospirillum ferriphilum (bacteria)
Methodsingle particle reconstruction / Resolution: 3.52 Å
AuthorsLiu RH / Liu JD / Zhang K / He SJ / Feng QS / Dai J / Guo XR / Fu Y / Li Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of Leptospirillum ferriphilum helicase Dda
Authors: Liu RH / Liu JD / Zhang K / He SJ / Feng QS / Dai J / Guo XR / Fu Y / Li Y
History
DepositionDec 5, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62609.png

Downloads & links

-
Map

FileDownload / File: emd_62609.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.67 Å/pix.
x 480 pix.
= 320.64 Å		0.67 Å/pix.
x 480 pix.
= 320.64 Å		0.67 Å/pix.
x 480 pix.
= 320.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-37.883353999999997 - 67.486534000000006
Average (Standard dev.)0.000000000002111 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 320.63998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62609_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62609_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LfDda

EntireName: LfDda
Components
  • Complex: LfDda
    • Protein or peptide: Putative deoxyribonuclease

-
Supramolecule #1: LfDda

SupramoleculeName: LfDda / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leptospirillum ferriphilum (strain ML-04) (bacteria)

-
Macromolecule #1: Putative deoxyribonuclease

MacromoleculeName: Putative deoxyribonuclease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leptospirillum ferriphilum (bacteria) / Strain: ML-04
Molecular weightTheoretical: 47.59716 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSLTLTSDQ ENALEGMKAF CANSLDKNWP AALLQGYAGT GKTTLLGVLV SSLVEKGYKV AVTAPTNKAV SVLMEKVPDA SCHATIHSL LGLALQEEGE TQKLVSSGTS CVNDFDVVIV DECSMIGADL LSMIRGRPKF IFVGDPAQLP PVNEIFSPVF R SVGLRWSL ...String:
MNSLTLTSDQ ENALEGMKAF CANSLDKNWP AALLQGYAGT GKTTLLGVLV SSLVEKGYKV AVTAPTNKAV SVLMEKVPDA SCHATIHSL LGLALQEEGE TQKLVSSGTS CVNDFDVVIV DECSMIGADL LSMIRGRPKF IFVGDPAQLP PVNEIFSPVF R SVGLRWSL SKIVRQAEGN AIIDLSAEIR LKSEEGVPMT LEDIKSILEG KLEACCMSGI DLVSALTHEW KEGRDSRILA WR NATVDFY NRAIFSSLYP DATTPFVPGQ TAIVGSSFEV DPDAHVRLDT SEEVTILSLE PGERLGVPVF LARVQRASGE TWT LPIPRS SSDFAREVKA SFSEWRFWKN QVKASPSASE ASEADRKASA FLKKGWALKK GIADLRHPWA MTVHKAQGST YDTV FVDWN DLRAIPSDDF LRILYTAVTR PSRYLAICH

UniProtKB: Putative deoxyribonuclease

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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