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- EMDB-71448: Cryo-EM structure of the engineered HflK/C variant stabilized in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-71448
TitleCryo-EM structure of the engineered HflK/C variant stabilized in the closed conformation via disulfide bond crosslinking.
Map data
Sample
  • Complex: HflK.HflKC complex
    • Protein or peptide: Protein HflK
    • Protein or peptide: Modulator of FtsH protease HflC
KeywordsFtsH / HflK / HflC / CHAPERONE / AAA protease
Function / homology
Function and homology information


membrane / plasma membrane
Similarity search - Function
HflC / HflK / Menbrane protein HflK, N-terminal / Bacterial membrane protein N terminal / : / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Modulator of FtsH protease HflC / Protein HflK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsIqbal N / Ghanbarpour A
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the overexpressed HflK.HflC complex
Authors: Ghanbarpour A / Sauer RT / Davis JH
History
DepositionJun 25, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71448.png

Downloads & links

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Map

FileDownload / File: emd_71448.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 384 pix.
= 442.867 Å		1.15 Å/pix.
x 384 pix.
= 442.867 Å		1.15 Å/pix.
x 384 pix.
= 442.867 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.235
Minimum - Maximum-0.94078994 - 1.8932878
Average (Standard dev.)0.00038670536 (±0.052189786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 442.86722 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71448_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71448_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71448_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 : HflK.HflKC complex

EntireName: HflK.HflKC complex
Components
  • Complex: HflK.HflKC complex
    • Protein or peptide: Protein HflK
    • Protein or peptide: Modulator of FtsH protease HflC

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Supramolecule #1: HflK.HflKC complex

SupramoleculeName: HflK.HflKC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21

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Macromolecule #1: Protein HflK

MacromoleculeName: Protein HflK / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.662918 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAWNQPGNNG QDRDPWGSSK PGGNSEGNGN KGGRDQGPPD LDDIFRKLSK KLGGLGGGKG TGSGGGSSSQ GPRPQLGGRV VTIAAAAIV IIWAASGFYT IKEAERGVVT RFGKFSHLVE PGLNWKPTFI DEVKPVNVEA VRELAASGVM LTSDENVVRV E MNVQYRVT ...String:
MAWNQPGNNG QDRDPWGSSK PGGNSEGNGN KGGRDQGPPD LDDIFRKLSK KLGGLGGGKG TGSGGGSSSQ GPRPQLGGRV VTIAAAAIV IIWAASGFYT IKEAERGVVT RFGKFSHLVE PGLNWKPTFI DEVKPVNVEA VRELAASGVM LTSDENVVRV E MNVQYRVT NPEKYLYSVT SPDDSLRQAT DSALRGVIGK YTMDRILTEG RTVIRSDTQR ELEETIRPYD MGITLLDVNF QA ARPPEEV KAAFDDAIAA RENEQQYIRE AECYTNEVQP RANGQCQRIL EEARAYKAQT ILEAQGEVAR FAKLLPEYKA APE ITRERL YIETMEKVLG NTRKVLVNDK GGNLMVLPLD QMLKGGNAPA AKSDNGASNL LRLPPASSST TSGASNTSST SQGD IMDQR RANAQRNDYQ RQGE

UniProtKB: Protein HflK

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Macromolecule #2: Modulator of FtsH protease HflC

MacromoleculeName: Modulator of FtsH protease HflC / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 37.768012 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRKSVIAIII IVLVVLYMSV FVVKEGERGI TLRFGKVLRD DDNKPLVYEP GLHFKIPFIE TVKMLDARIQ TMDNQADRFV TKEKKDLIV DSYIKWRISD FSRYYLATGG GDISQAEVLL KRKFSDRLRS EIGRLDVKDI VTDSRGRLTL EVRDALNSGS A GTEDEVTT ...String:
MRKSVIAIII IVLVVLYMSV FVVKEGERGI TLRFGKVLRD DDNKPLVYEP GLHFKIPFIE TVKMLDARIQ TMDNQADRFV TKEKKDLIV DSYIKWRISD FSRYYLATGG GDISQAEVLL KRKFSDRLRS EIGRLDVKDI VTDSRGRLTL EVRDALNSGS A GTEDEVTT PAADNAIAEA AERVTAETKG KVPVINPNSM AALGIEVVDV RIKQINLPTE VSEAIYNRMR AERECVARRH RS QGQEEAE KLRATADYEV TRTLAECERQ GRIMRGEGDA EAAKLFADAF SKDPDFYAFI RSLRAYENSF SGNQDVMVMS PDS DFFRYM KTPTSATR

UniProtKB: Modulator of FtsH protease HflC

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.19 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v.4.6) / Details: Patch CTF estimation, cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.6) / Number images used: 299919
Initial angle assignmentType: PROJECTION MATCHING / Details: Ab-initio reconstruction, cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v.4.6)

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