[English] 日本語
Yorodumi
- EMDB-75463: ArsB from L. ferriphilum in inward-facing state (antiparallel dimer) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75463
TitleArsB from L. ferriphilum in inward-facing state (antiparallel dimer)
Map data
Sample
  • Complex: ArsB in inward-facing state
    • Protein or peptide: Arsenical pump membrane protein
Keywordsarsenite / membrane transporter / secondary transporter / MEMBRANE PROTEIN
Function / homologyarsenite secondary active transmembrane transporter activity / antimonite secondary active transmembrane transporter activity / Arsenical pump membrane protein, ArsB / Arsenical pump membrane protein / response to arsenic-containing substance / plasma membrane / Arsenical pump membrane protein
Function and homology information
Biological speciesLeptospirillum ferriphilum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMahajan S / Clemons WM / Rees DC
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: Structural basis of metalloid transport by the arsenite efflux pump ArsB
Authors: Mahajan S / Demirer K / Clemons WM / Rees DC
History
DepositionFeb 8, 2026-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75463.png

Downloads & links

-
Map

FileDownload / File: emd_75463.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 448 pix.
= 291.2 Å		0.65 Å/pix.
x 448 pix.
= 291.2 Å		0.65 Å/pix.
x 448 pix.
= 291.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3041329 - 0.44268563
Average (Standard dev.)0.00016540346 (±0.010251773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: unsharpened map

Fileemd_75463_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75463_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_75463_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ArsB in inward-facing state

EntireName: ArsB in inward-facing state
Components
  • Complex: ArsB in inward-facing state
    • Protein or peptide: Arsenical pump membrane protein

-
Supramolecule #1: ArsB in inward-facing state

SupramoleculeName: ArsB in inward-facing state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leptospirillum ferriphilum (bacteria) / Strain: ML-04

-
Macromolecule #1: Arsenical pump membrane protein

MacromoleculeName: Arsenical pump membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leptospirillum ferriphilum (bacteria) / Strain: ML-04
Molecular weightTheoretical: 47.082609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLLALLIFLA TIVLVIWQPR GLGIGWSATL GAVAALLSGV VHIGDIPVVW QIVWNATATF IAIIIISLLL DEAGFFEWAA LHVARRGKG KGHLLFVLIV LLGASVAALF ANDGAALILT PIVMAMLLAL GFSPSATLAF VMAAGFIADT ASLPLVVSNL V NIVSADFF ...String:
MLLALLIFLA TIVLVIWQPR GLGIGWSATL GAVAALLSGV VHIGDIPVVW QIVWNATATF IAIIIISLLL DEAGFFEWAA LHVARRGKG KGHLLFVLIV LLGASVAALF ANDGAALILT PIVMAMLLAL GFSPSATLAF VMAAGFIADT ASLPLVVSNL V NIVSADFF KIGFNDYAAV MIPVDIVAII ASLTVLSFYF RRSIPWHYDV NQLKQPNEAI RDVATFRIGW IVLVLLLVGF FG LEPLGVP VSAVAAAGAL LLLAVAARGH VISTRKVLRE APWQIVVFSL GMYLVVYGLR NQGLAGHIAR LLDYFAQGGV WGA ALGTGF LTALLSSAMN NMPTVLVGAL SIDATSASGV VKNAMIYANV IGSDLGPKIT PIGSLATLLW LHVLARKDMT ITWG YYFKV GVVLTVPVLA VTLAALALRL SLAGSGSGSG SGSGGSGSLE VLFQ

UniProtKB: Arsenical pump membrane protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 57278
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