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- PDB-9paw: Cryo-EM structure of the engineered HflK/C variant stabilized in ... -

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Basic information

Entry
Database: PDB / ID: 9paw
TitleCryo-EM structure of the engineered HflK/C variant stabilized in the closed conformation via disulfide bond crosslinking.
Components
  • Modulator of FtsH protease HflC
  • Protein HflK
KeywordsCHAPERONE / FtsH / HflK / HflC / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsIqbal, N. / Ghanbarpour, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the overexpressed HflK.HflC complex
Authors: Ghanbarpour, A. / Sauer, R.T. / Davis, J.H.
History
DepositionJun 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
XA: Protein HflK
XB: Modulator of FtsH protease HflC
XC: Protein HflK
XD: Modulator of FtsH protease HflC
XE: Protein HflK
XF: Modulator of FtsH protease HflC
XG: Protein HflK
XH: Modulator of FtsH protease HflC
XI: Protein HflK
XJ: Modulator of FtsH protease HflC
XK: Protein HflK
XL: Modulator of FtsH protease HflC
XM: Protein HflK
XN: Modulator of FtsH protease HflC
XO: Protein HflK
XP: Modulator of FtsH protease HflC
XQ: Protein HflK
XR: Modulator of FtsH protease HflC
XS: Protein HflK
XT: Modulator of FtsH protease HflC
XU: Protein HflK
XV: Modulator of FtsH protease HflC
XW: Protein HflK
XX: Modulator of FtsH protease HflC


Theoretical massNumber of molelcules
Total (without water)1,001,17124
Polymers1,001,17124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Protein HflK


Mass: 45662.918 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hflK, Z5781, ECs5150 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABC8
#2: Protein
Modulator of FtsH protease HflC


Mass: 37768.012 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hflC, Z5782, ECs5151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABC5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HflK.HflKC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1750 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47.19 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv. 4.7particle selection
4cryoSPARCv.4.6CTF correction
11cryoSPARCv.4.6final Euler assignment
13cryoSPARCv.4.63D reconstruction
CTF correctionDetails: Patch CTF estimation, cryoSPARC / Type: NONE
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299919 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00152613
ELECTRON MICROSCOPYf_angle_d0.36470920
ELECTRON MICROSCOPYf_dihedral_angle_d0.767284
ELECTRON MICROSCOPYf_chiral_restr0.0387869
ELECTRON MICROSCOPYf_plane_restr0.0039359

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