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- PDB-8hzt: Bacillus subtilis SepF protein assembly (G137N mutant) -

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Basic information

Entry
Database: PDB / ID: 8hzt
TitleBacillus subtilis SepF protein assembly (G137N mutant)
ComponentsCell division protein SepF
KeywordsPROTEIN FIBRIL / Cell division / Fibril assembly / Single point mutation
Function / homology:
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLID-STATE NMR / DGSA-distance geometry simulated annealing
AuthorsLiu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Molecular basis for curvature formation in SepF polymerization.
Authors: Wenjing Liu / Chang Zhang / Huawei Zhang / Shaojie Ma / Jing Deng / Daping Wang / Ziwei Chang / Jun Yang /
Abstract: The self-assembly of proteins into curved structures plays an important role in many cellular processes. One good example of this phenomenon is observed in the septum-forming protein (SepF), which ...The self-assembly of proteins into curved structures plays an important role in many cellular processes. One good example of this phenomenon is observed in the septum-forming protein (SepF), which forms polymerized structures with uniform curvatures. SepF is essential for regulating the thickness of the septum during bacteria cell division. In , SepF polymerization involves two distinct interfaces, the β-β and α-α interfaces, which define the assembly unit and contact interfaces, respectively. However, the mechanism of curvature formation in this step is not yet fully understood. In this study, we employed solid-state NMR (SSNMR) to compare the structures of cyclic wild-type SepF assemblies with linear assemblies resulting from a mutation of G137 on the β-β interface. Our results demonstrate that while the sequence differences arise from the internal assembly unit, the dramatic changes in the shape of the assemblies depend on the α-α interface between the units. We further provide atomic-level insights into how the angular variation of the α2 helix on the α-α interface affects the curvature of the assemblies, using a combination of SSNMR, cryo-electron microscopy, and simulation methods. Our findings shed light on the shape control of protein assemblies and emphasize the importance of interhelical contacts in retaining curvature.
History
DepositionJan 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein SepF
B: Cell division protein SepF


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,8102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2640 Å2
ΔGint-14 kcal/mol
Surface area8550 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cell division protein SepF


Mass: 8905.079 Da / Num. of mol.: 2 / Mutation: G137N
Source method: isolated from a genetically manipulated source
Details: SepF was truncated to 57-151 of assembly state to accomplish the SSNMR experiments; sequence from 60 to 139 was chosen which included all the assigned section of chain A and B for dimer ...Details: SepF was truncated to 57-151 of assembly state to accomplish the SSNMR experiments; sequence from 60 to 139 was chosen which included all the assigned section of chain A and B for dimer calculation during CS-Rosetta structure calculation
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: sepF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A857HFW2

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NCA
121isotropic12D DARR
131isotropic13D NCACX
141isotropic13D NCOCX
151isotropic13D CONCA

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Sample preparation

DetailsType: solid / Contents: 66% w/w 15N/13C SepF G137N mutant, ethanol/water
Details: 15N/13C labeled SepF assembly 57-151 (G137N mutant) for solid-state NMR (ssNMR)
Label: 15N/13C / Solvent system: ethanol/water
SampleConc.: 66 % w/w / Component: SepF G137N mutant / Isotopic labeling: 15N/13C
Sample conditionsIonic strength: 0 M / Label: 15N/13C / pH: 8.5 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Varian SepF Assembly 57 151 G137N mutant / Manufacturer: Varian / Model: SepF Assembly 57 151 G137N mutant / Field strength: 600 MHz / Details: with 3.2 BIOMAS probe

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20000 / Conformers submitted total number: 10

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