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- PDB-25fq: BAM-SurA complex (Core only) -

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Basic information

Entry
Database: PDB / ID: 25fq
TitleBAM-SurA complex (Core only)
Components
  • Chaperone SurA,Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamB
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
KeywordsPROTEIN TRANSPORT / Outer membrane protein / Periplasmic chaperon
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / peptide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / outer membrane-bounded periplasmic space / protein folding ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / peptide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / outer membrane-bounded periplasmic space / protein folding / protein-macromolecule adaptor activity / protein stabilization / cell surface / membrane / identical protein binding
Similarity search - Function
Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / Trigger factor/SurA domain superfamily / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain ...Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / Trigger factor/SurA domain superfamily / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamB / BamE-like / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamA / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / 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 BamA / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Chaperone SurA / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKohga, H. / Miyazaki, R. / Tsukazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of the SurA-BAM complex reveal conformational changes in outer membrane protein assembly.
Authors: Ryoji Miyazaki / Hidetaka Kohga / Nami Matsuoka / Yuki Maruno / Wataru Yoshimoto / Yutaro S Takahashi / Dede Heri Yuli Yanto / Yudhi Nugraha / Hideki Shigematsu / Takuya Shiota / Tomoya Tsukazaki /
Abstract: The outer membrane (OM) of Gram-negative bacteria acts as a permeability barrier against toxic compounds. Its integrity is maintained by various outer membrane proteins (OMPs), which are inserted ...The outer membrane (OM) of Gram-negative bacteria acts as a permeability barrier against toxic compounds. Its integrity is maintained by various outer membrane proteins (OMPs), which are inserted into the OM by the β-barrel assembly machinery (BAM) complex. The periplasmic chaperone SurA delivers unfolded OMPs to BAM; however, the mechanism of substrate transfer remains unclear. Here, we show that the flexible P1 and P2 domains of SurA regulate the function of its Core domain and interact with BAM components, including BamE, whose interaction with the P2 domain is crucial for efficient OMP assembly. Moreover, cryo-electron microscopy reveals four distinct Escherichia coli SurA-BAM structures, suggesting dynamic domain rearrangements of SurA. Based on these findings, we propose a dynamic model in which SurA transfers substrates to BAM through multiple conformational changes, providing a unified framework for chaperone-assisted OMP biogenesis.
History
DepositionApr 1, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone SurA,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,Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)392,3726
Polymers392,3726
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 Chaperone SurA,Outer membrane protein assembly factor BamA / Peptidyl-prolyl cis-trans isomerase SurA / PPIase SurA / Rotamase SurA


Mass: 136094.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SurA-BamA fusion protein,SurA-BamA fusion protein / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: surA, Z0062, ECs0058, bamA, yaeT, EcE24377A_0181 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABZ8, UniProt: A7ZHR7, peptidylprolyl isomerase
#2: Protein Outer membrane protein assembly factor BamB


Mass: 41918.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 36875.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamD


Mass: 27858.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD, yfiO, Z3889, ECs3458 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC04
#5: Protein Outer membrane protein assembly factor BamE


Mass: 13530.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamE, smpA, c3139 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A938
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

Component
IDNameTypeEntity IDParent-IDSource
1BAM-SurA complex (Core only)COMPLEXall0RECOMBINANT
2BAM complexCOMPLEXall1RECOMBINANT
3Chaperone SurACOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
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

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107150 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01615104
ELECTRON MICROSCOPYf_angle_d0.720503
ELECTRON MICROSCOPYf_dihedral_angle_d5.9992115
ELECTRON MICROSCOPYf_chiral_restr0.0452261
ELECTRON MICROSCOPYf_plane_restr0.0042703

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