[English] 日本語
Yorodumi
- EMDB-63950: Cryo-EM structure of Leminorella grimontii GatC in the presence o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63950
TitleCryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose
Map data
Sample
  • Complex: GatC bound to D-xylose
    • Protein or peptide: PTS galactitol transporter subunit IIC
KeywordsPTS / D-xylose / transporter / TRANSPORT PROTEIN
Function / homologygalactitol transmembrane transporter activity / Galactitol permease IIC component / Phosphotransferase system, sugar-specific permease component / PTS system sugar-specific permease component / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / phosphoenolpyruvate-dependent sugar phosphotransferase system / plasma membrane / PTS galactitol transporter subunit IIC
Function and homology information
Biological speciesLeminorella grimontii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsTakahashi YS / Kohga H / Shigematsu H / Miyazaki R / Tsukazaki T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis of a phosphotransferase system xylose transporter
Authors: Takahashi YS / Kohga H / Chek MF / Yamamoto K / Takahashi JF / Shigematsu H / Tanaka Y / Ichikawa M / Miyazaki R / Hakoshima T / Tsukazaki T
History
DepositionMar 25, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63950.png

Downloads & links

-
Map

FileDownload / File: emd_63950.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 256 pix.
= 192.512 Å		0.75 Å/pix.
x 256 pix.
= 192.512 Å		0.75 Å/pix.
x 256 pix.
= 192.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.054445285 - 0.16226229
Average (Standard dev.)0.0019070157 (±0.0069777314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 192.512 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_63950_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63950_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GatC bound to D-xylose

EntireName: GatC bound to D-xylose
Components
  • Complex: GatC bound to D-xylose
    • Protein or peptide: PTS galactitol transporter subunit IIC

-
Supramolecule #1: GatC bound to D-xylose

SupramoleculeName: GatC bound to D-xylose / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leminorella grimontii (bacteria)

-
Macromolecule #1: PTS galactitol transporter subunit IIC

MacromoleculeName: PTS galactitol transporter subunit IIC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leminorella grimontii (bacteria)
Molecular weightTheoretical: 50.078062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFTEIMRYVL DLGPTVMLPI VVILFSLLLK MKPGDAFKSG IHIGIGFVGI GLVIGLMLDS IGPAAKAMAE AFDINLKVVD IGWPGSSPM TWASQIALIA IPIAIVVNLV MLMTRMTRVV NVDIWNIWHM TFTGALVHIA TGSYALAIVG VVVHAAFVYK L GDWFAKDT ...String:
MFTEIMRYVL DLGPTVMLPI VVILFSLLLK MKPGDAFKSG IHIGIGFVGI GLVIGLMLDS IGPAAKAMAE AFDINLKVVD IGWPGSSPM TWASQIALIA IPIAIVVNLV MLMTRMTRVV NVDIWNIWHM TFTGALVHIA TGSYALAIVG VVVHAAFVYK L GDWFAKDT RDFFGLDGIA IPHGTSAYLG PIAVLVDTVI EKIPGLNRIH FSADDVQKRF GAFGEPVTIG FVMGLVIGLL AG YEIKAVL QLAVKTAAVM LLMPRVIKPI MDGLTPIAKQ ARSRLQAKFG GQDFLIGLDP ALLLGHTSVV SASLIFIPLT ILI AVVTPG NQVLPFGDLA TIGFFVAMAV AVHQGNLFRT LISGVIIMSI TLWIATQTIG LHTQLAANAG SLTGDGSLVA SMDQ GGSPI TYLLVQALTL ENVIGLVAIG ALYGIGIFLT WRRAKRFAAQ AESPANVQVQ AAGQSLESSG ENLYFQ

UniProtKB: PTS galactitol transporter subunit IIC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7 / Details: 300mM NaCl, 50mM HEPES-NaOH (pH7.0), 10mM D-xylose
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm

+
Image processing

Particle selectionNumber selected: 2480272
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 442864
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
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