[English] 日本語
Yorodumi
- PDB-7wi3: Cryo-EM structure of E.Coli FtsH-HflkC AAA protease complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wi3
TitleCryo-EM structure of E.Coli FtsH-HflkC AAA protease complex
Components
  • ATP-dependent zinc metalloprotease FtsH
  • Modulator of FtsH protease HflC
  • Modulator of FtsH protease HflK
KeywordsMEMBRANE PROTEIN / complex
Function / homology
Function and homology information


: / membrane protein complex / negative regulation of peptidase activity / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / response to heat / ATP hydrolysis activity ...: / membrane protein complex / negative regulation of peptidase activity / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / response to heat / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane / cytosol
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 / Peptidase M41, FtsH extracellular ...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 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent zinc metalloprotease FtsH / Modulator of FtsH protease HflC / Modulator of FtsH protease HflK
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsQiao, Z. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Cell Rep / Year: 2022
Title: Cryo-EM structure of the entire FtsH-HflKC AAA protease complex.
Authors: Zhu Qiao / Tatsuhiko Yokoyama / Xin-Fu Yan / Ing Tsyr Beh / Jian Shi / Sandip Basak / Yoshinori Akiyama / Yong-Gui Gao /
Abstract: The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic ...The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic activity. Here, we present structure of the entire FtsH-HflKC complex, comprising 12 copies of both HflK and HflC, all of which interact reciprocally to form a cage, as well as four FtsH hexamers with periplasmic domains and transmembrane helices enclosed inside the cage and cytoplasmic domains situated at the base of the cage. FtsH K61/D62/S63 in the β2-β3 loop in the periplasmic domain directly interact with HflK, contributing to complex formation. Pull-down and in vivo enzymatic activity assays validate the importance of the interacting interface for FtsH-HflKC complex formation. Structural comparison with the substrate-bound human m-AAA protease AFG3L2 offers implications for the HflKC cage in modulating substrate access to FtsH. Together, our findings provide a better understanding of FtsH-type AAA protease holoenzyme assembly and regulation.
History
DepositionJan 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Modulator of FtsH protease HflC
B: Modulator of FtsH protease HflK
C: Modulator of FtsH protease HflC
D: Modulator of FtsH protease HflC
E: ATP-dependent zinc metalloprotease FtsH
F: Modulator of FtsH protease HflK
G: Modulator of FtsH protease HflK
H: ATP-dependent zinc metalloprotease FtsH
I: ATP-dependent zinc metalloprotease FtsH
J: ATP-dependent zinc metalloprotease FtsH
K: ATP-dependent zinc metalloprotease FtsH
L: ATP-dependent zinc metalloprotease FtsH
Y: Modulator of FtsH protease HflC
a: Modulator of FtsH protease HflK
c: Modulator of FtsH protease HflC
e: Modulator of FtsH protease HflC
g: ATP-dependent zinc metalloprotease FtsH
i: Modulator of FtsH protease HflK
k: Modulator of FtsH protease HflK
m: ATP-dependent zinc metalloprotease FtsH
o: ATP-dependent zinc metalloprotease FtsH
q: ATP-dependent zinc metalloprotease FtsH
s: ATP-dependent zinc metalloprotease FtsH
u: ATP-dependent zinc metalloprotease FtsH
Z: Modulator of FtsH protease HflC
b: Modulator of FtsH protease HflK
d: Modulator of FtsH protease HflC
f: Modulator of FtsH protease HflC
h: ATP-dependent zinc metalloprotease FtsH
j: Modulator of FtsH protease HflK
l: Modulator of FtsH protease HflK
n: ATP-dependent zinc metalloprotease FtsH
p: ATP-dependent zinc metalloprotease FtsH
r: ATP-dependent zinc metalloprotease FtsH
t: ATP-dependent zinc metalloprotease FtsH
v: ATP-dependent zinc metalloprotease FtsH
M: Modulator of FtsH protease HflC
N: Modulator of FtsH protease HflK
O: Modulator of FtsH protease HflC
P: Modulator of FtsH protease HflC
Q: ATP-dependent zinc metalloprotease FtsH
R: Modulator of FtsH protease HflK
S: Modulator of FtsH protease HflK
T: ATP-dependent zinc metalloprotease FtsH
U: ATP-dependent zinc metalloprotease FtsH
V: ATP-dependent zinc metalloprotease FtsH
W: ATP-dependent zinc metalloprotease FtsH
X: ATP-dependent zinc metalloprotease FtsH


Theoretical massNumber of molelcules
Total (without water)2,698,76148
Polymers2,698,76148
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Modulator of FtsH protease HflC


Mass: 37703.887 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: hflC, hflA, b4175, JW4133 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABC3
#2: Protein
Modulator of FtsH protease HflK


Mass: 45598.793 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: hflK, hflA, b4174, JW4132 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABC7
#3: Protein ...
ATP-dependent zinc metalloprotease FtsH / Cell division protease FtsH


Mass: 70797.031 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ftsH, hflB, mrsC, std, tolZ, b3178, JW3145 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAI3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: E.Coli protein complexEscherichia coli / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26863 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 106.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010470396
ELECTRON MICROSCOPYf_angle_d1.158695129
ELECTRON MICROSCOPYf_chiral_restr0.137910792
ELECTRON MICROSCOPYf_plane_restr0.006712416
ELECTRON MICROSCOPYf_dihedral_angle_d20.879826920

+
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