[English] 日本語
Yorodumi
- EMDB-39773: Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39773
TitleCryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ
Map data
Sample
  • Complex: QmcA-YbbJ complex
    • Protein or peptide: Protein QmcA
    • Protein or peptide: Inner membrane protein YbbJ
Keywordscomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


identical protein binding / plasma membrane
Similarity search - Function
: / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues ...: / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Protein QmcA / Inner membrane protein YbbJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQiao Z / Gao YG
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Structure / Year: 2024
Title: Cryo-EM structure of the SPFH-NfeD family protein complex QmcA-YbbJ.
Authors: Kwan Ann Tan / Zhu Qiao / Zachary Ze En Lim / Joshua Yi Yeo / Yonlada Yong / Phong Hoa Do / Rya Ero / Yong-Gui Gao /
Abstract: The SPFH (stomatin, prohibitin, flotillin, and HflK/C) protein family is universally present and encompasses the evolutionarily conserved SPFH domain. These proteins are predominantly localized in ...The SPFH (stomatin, prohibitin, flotillin, and HflK/C) protein family is universally present and encompasses the evolutionarily conserved SPFH domain. These proteins are predominantly localized in lipid raft and implicated in various biological processes. The NfeD (nodulation formation efficiency D) protein family is often encoded in tandem with SPFH proteins, suggesting a close functional relationship. Here, we elucidate the cryoelectron microscopy (cryo-EM) structure of the Escherichia coli QmcA-YbbJ complex belonging to the SPFH and NfeD families, respectively. Our findings reveal that the QmcA-YbbJ complex forms an intricate cage-like structure composed of 26 copies of QmcA-YbbJ heterodimers. The transmembrane helices of YbbJ act as adhesive elements bridging adjacent QmcA molecules, while the oligosaccharide-binding domain of YbbJ encapsulates the SPFH domain of QmcA. Our structural study significantly contributes to understanding the functional role of the NfeD protein family and sheds light on the interplay between SPFH and NfeD family proteins.
History
DepositionApr 18, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39773.png

Downloads & links

-
Map

FileDownload / File: emd_39773.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.)
1.46 Å/pix.
x 256 pix.
= 373.76 Å		1.46 Å/pix.
x 256 pix.
= 373.76 Å		1.46 Å/pix.
x 256 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0018179584 - 1.9883393
Average (Standard dev.)0.0038183292 (±0.043962277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_39773_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39773_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : QmcA-YbbJ complex

EntireName: QmcA-YbbJ complex
Components
  • Complex: QmcA-YbbJ complex
    • Protein or peptide: Protein QmcA
    • Protein or peptide: Inner membrane protein YbbJ

-
Supramolecule #1: QmcA-YbbJ complex

SupramoleculeName: QmcA-YbbJ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Protein QmcA

MacromoleculeName: Protein QmcA / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 33.778023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLIFIPILIF VALVIVGAGV KIVPQGYQWT VERFGRYTKT LQPGLSLVVP FMDRIGRKIN MMEQVLDIPS QEVISKDNAN VTIDAVCFI QVIDAPRAAY EVSNLELAII NLTMTNIRTV LGSMELDEML SQRDSINSRL LRIVDEATNP WGIKVTRIEI R DVRPPAEL ...String:
MLIFIPILIF VALVIVGAGV KIVPQGYQWT VERFGRYTKT LQPGLSLVVP FMDRIGRKIN MMEQVLDIPS QEVISKDNAN VTIDAVCFI QVIDAPRAAY EVSNLELAII NLTMTNIRTV LGSMELDEML SQRDSINSRL LRIVDEATNP WGIKVTRIEI R DVRPPAEL ISSMNAQMKA ERTKRAYILE AEGIRQAEIL KAEGEKQSQI LKAEGERQSA FLQAEARERS AEAEARATKM VS EAIASGD IQAVNYFVAQ KYTEALQQIG SSSNSKVVMM PLEASSLMGS IAGIAELVKD SANKRTQP

UniProtKB: Protein QmcA

-
Macromolecule #2: Inner membrane protein YbbJ

MacromoleculeName: Inner membrane protein YbbJ / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 16.956775 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MMELMVVHPH IFWLSLGGLL LAAEMLGGNG YLLWSGVAAV ITGLVVWLVP LGWEWQGVMF AILTLLAAWL WWKWLSRRVR EQKHSDSHL NQRGQQLIGR RFVLESPLVN GRGHMRVGDS SWPVSASEDL GAGTHVEVIA IEGITLHIRA VSS

UniProtKB: Inner membrane protein YbbJ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36372
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