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- PDB-8z5g: Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ -

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Basic information

Entry
Database: PDB / ID: 8z5g
TitleCryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ
Components
  • Inner membrane protein YbbJ
  • Protein QmcA
KeywordsMEMBRANE PROTEIN / complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQiao, Z. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Structure / Year: 2024
Title: Cryo-EM structure of the SPFH-NfeD family protein complex QmcA-YbbJ.
Authors: Kwan Ann Tan / Zhu Qiao / Zachary Ze En Lim / Joshua Yi Yeo / Yonlada Yong / Phong Hoa Do / Ero Rya / Yong-Gui Gao /
Abstract: The SPFH (stomatin, prohibitin, flotillin, and HflK/C) protein family is universally present and encompasses the evolutionarily conserved SPFH domain. These proteins are predominantly localized in ...The SPFH (stomatin, prohibitin, flotillin, and HflK/C) protein family is universally present and encompasses the evolutionarily conserved SPFH domain. These proteins are predominantly localized in lipid raft and implicated in various biological processes. The NfeD (nodulation formation efficiency D) protein family is often encoded in tandem with SPFH proteins, suggesting a close functional relationship. Here, we elucidate the cryoelectron microscopy (cryo-EM) structure of the Escherichia coli QmcA-YbbJ complex belonging to the SPFH and NfeD families, respectively. Our findings reveal that the QmcA-YbbJ complex forms an intricate cage-like structure composed of 26 copies of QmcA-YbbJ heterodimers. The transmembrane helices of YbbJ act as adhesive elements bridging adjacent QmcA molecules, while the oligosaccharide-binding domain of YbbJ encapsulates the SPFH domain of QmcA. Our structural study significantly contributes to understanding the functional role of the NfeD protein family and sheds light on the interplay between SPFH and NfeD family proteins.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein QmcA
B: Inner membrane protein YbbJ
C: Protein QmcA
D: Inner membrane protein YbbJ
E: Protein QmcA
F: Inner membrane protein YbbJ
G: Protein QmcA
H: Inner membrane protein YbbJ
I: Protein QmcA
J: Inner membrane protein YbbJ
K: Protein QmcA
L: Inner membrane protein YbbJ
M: Protein QmcA
N: Inner membrane protein YbbJ
O: Protein QmcA
P: Inner membrane protein YbbJ
Q: Protein QmcA
R: Inner membrane protein YbbJ
S: Protein QmcA
T: Inner membrane protein YbbJ
V: Protein QmcA
W: Inner membrane protein YbbJ
X: Protein QmcA
Y: Inner membrane protein YbbJ
Z: Protein QmcA
AA: Inner membrane protein YbbJ
BA: Protein QmcA
CA: Inner membrane protein YbbJ
DA: Protein QmcA
EA: Inner membrane protein YbbJ
FA: Protein QmcA
GA: Inner membrane protein YbbJ
HA: Protein QmcA
IA: Inner membrane protein YbbJ
JA: Protein QmcA
KA: Inner membrane protein YbbJ
LA: Protein QmcA
MA: Inner membrane protein YbbJ
NA: Protein QmcA
OA: Inner membrane protein YbbJ
PA: Protein QmcA
QA: Inner membrane protein YbbJ
RA: Protein QmcA
SA: Inner membrane protein YbbJ
TA: Protein QmcA
UA: Inner membrane protein YbbJ
VA: Protein QmcA
WA: Inner membrane protein YbbJ
XA: Protein QmcA
YA: Inner membrane protein YbbJ
ZA: Protein QmcA
AB: Inner membrane protein YbbJ


Theoretical massNumber of molelcules
Total (without water)1,319,10552
Polymers1,319,10552
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 QmcA


Mass: 33778.023 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: qmcA, ybbK, b0489, JW0478 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA53
#2: Protein ...
Inner membrane protein YbbJ


Mass: 16956.775 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ybbJ, b0488, JW5065 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAS3
Has protein modificationN

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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: QmcA-YbbJ complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36372 / Symmetry type: POINT

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