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- EMDB-39773: Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ -

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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 / 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 / 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 E.coli SPFH-NfeD family protein complex QmcA-YbbJ.
Authors: Qiao Z / Gao YG
History
DepositionApr 18, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39773.png

Downloads & links

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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 °

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Supplemental data

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Half map: #2

Fileemd_39773_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39773_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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)

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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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

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