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- PDB-9hg6: BAM-SurA complex in the swing-in state -

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Basic information

Entry
Database: PDB / ID: 9hg6
TitleBAM-SurA complex in the swing-in state
Components
  • (Outer membrane protein assembly factor ...) x 5
  • Chaperone SurA
KeywordsMEMBRANE PROTEIN / insertase / outer membrane protein / chaperone / protein folding / protein complex
Function / homology
Function and homology information


: / maintenance of unfolded protein / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / : / peptide binding / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity ...: / maintenance of unfolded protein / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / : / peptide binding / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cell outer membrane / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / protein stabilization / cell adhesion / response to antibiotic / cell surface / identical protein binding / membrane
Similarity search - Function
Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA domain superfamily / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal ...Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA domain superfamily / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / Outer membrane protein assembly factor BamE domain / Outer membrane lipoprotein / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / BamE-like / Outer membrane protein assembly factor BamA / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Pyrrolo-quinoline quinone repeat / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / PQQ-like domain / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Chaperone SurA / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLehner, P.A. / Jakob, R.P. / Hiller, S.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation207755 Switzerland
Swiss National Science Foundation180541 Switzerland
CitationJournal: Sci Adv / Year: 2025
Title: Architecture and conformational dynamics of the BAM-SurA holo insertase complex.
Authors: Philippe A Lehner / Morris Degen / Roman P Jakob / Seyed Majed Modaresi / Morgane Callon / Björn M Burmann / Timm Maier / Sebastian Hiller /
Abstract: The proper folding of outer membrane proteins in Gram-negative bacteria relies on their delivery to the β-barrel assembly machinery (BAM) complex. The mechanism by which survival protein A (SurA), ...The proper folding of outer membrane proteins in Gram-negative bacteria relies on their delivery to the β-barrel assembly machinery (BAM) complex. The mechanism by which survival protein A (SurA), the major periplasmic chaperone, facilitates this process is not well understood. We determine the structure of the holo insertase complex, where SurA binds BAM for substrate delivery. High-resolution cryo-electron microscopy structures of four different states and a three-dimensional variability analysis show that the holo insertase complex has a large motional spectrum. SurA bound to BAM can undergo a large swinging motion between two states. This motion is uncoupled from the conformational flexibility of the BamA barrel, which can open and close without affecting SurA binding. Notably, we observed conformational coupling of the SurA swing state and the carboxyl-terminal helix grip domain of BamC. Substrate delivery by SurA to BAM appears to follow a concerted motion that encodes a gated delivery pathway through the BAM accessory proteins to the membrane entry site.
History
DepositionNov 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamB
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE
F: Chaperone SurA


Theoretical massNumber of molelcules
Total (without water)246,6656
Polymers246,6656
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

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Outer membrane protein assembly factor ... , 5 types, 5 molecules ABCDE

#1: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 88514.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P0A940
#2: Protein Outer membrane protein assembly factor BamB


Mass: 40924.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 34401.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamD


Mass: 25816.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P0AC02
#5: Protein Outer membrane protein assembly factor BamE


Mass: 11462.772 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P0A937

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Protein , 1 types, 1 molecules F

#6: Protein Chaperone SurA / Peptidyl-prolyl cis-trans isomerase SurA / PPIase SurA / Rotamase SurA / Survival protein A


Mass: 45545.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: surA, b0053, JW0052 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABZ6, peptidylprolyl isomerase

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Details

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: BAM-SurA insertase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 20mM Tris-HCl, 150mM NaCl, 0.05% DDM
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 289 K

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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 magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 68464
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1088801 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15LJO

5ljo

15LJO1PDBexperimental model
21AlphaFoldin silico model

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