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- EMDB-46056: Cryo-EM structure of a 'hat' portion of FtsH.HflK.HflC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-46056
TitleCryo-EM structure of a 'hat' portion of FtsH.HflK.HflC complex
Map data
Sample
  • Complex: FtsH.HflK.HflKC complex
    • Protein or peptide: Modulator of FtsH protease HflK
    • Protein or peptide: Modulator of FtsH protease HflC
KeywordsClpXP / full-engaged state / AAA protease / CHAPERONE
Function / homology
Function and homology information


peptidase activity / hydrolase activity / cell division / proteolysis / 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: 3.5 Å
AuthorsGhanbarpour A / Sauer RT / Davis JH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-GM144542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of a 'hat' portion of FtsH.HflK.HflC complex
Authors: Ghanbarpour A / Sauer RT / Davis JH
History
DepositionAug 3, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46056.png

Downloads & links

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Map

FileDownload / File: emd_46056.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 360 pix.
= 588.6 Å		1.64 Å/pix.
x 360 pix.
= 588.6 Å		1.64 Å/pix.
x 360 pix.
= 588.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0991
Minimum - Maximum-0.45867005 - 1.1563095
Average (Standard dev.)-0.0009965613 (±0.016423134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 588.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46056_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46056_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_46056_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 : FtsH.HflK.HflKC complex

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

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Supramolecule #1: FtsH.HflK.HflKC complex

SupramoleculeName: FtsH.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: Modulator of FtsH protease HflK

MacromoleculeName: Modulator of FtsH protease HflK / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.598793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 AEAYTNEVQP RANGQAQRIL 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: 37.703887 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 AEREAVARRH RS QGQEEAE KLRATADYEV TRTLAEAERQ 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.14 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: 0.05 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184019
Initial angle assignmentType: PROJECTION MATCHING / Details: Ab-initio reconstruction, cryoSPARC
Final angle assignmentType: PROJECTION MATCHING

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