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- EMDB-66834: BAM-SurA complex (P2-visible 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-66834
TitleBAM-SurA complex (P2-visible 1)
Map data
Sample
  • Complex: BAM-SurA complex (P2-visible 1)
    • Complex: BAM complex
      • Protein or peptide: Outer membrane protein assembly factor BamA
      • Protein or peptide: Outer membrane protein assembly factor BamB
      • Protein or peptide: Outer membrane protein assembly factor BamC
      • Protein or peptide: Outer membrane protein assembly factor BamD
      • Protein or peptide: Outer membrane protein assembly factor BamE
    • Complex: Chaperone SurA
      • Protein or peptide: Chaperone SurA
KeywordsOuter membrane protein / Periplasmic chaperon / PROTEIN TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsKohga H / Miyazaki R / Nugraha Y / Tsukazaki T
Funding support Japan, 1 items
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
DepositionOct 29, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66834.png

Downloads & links

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Map

FileDownload / File: emd_66834.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 432 pix.
= 328.32 Å		0.76 Å/pix.
x 432 pix.
= 328.32 Å		0.76 Å/pix.
x 432 pix.
= 328.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.1809812 - 0.4498115
Average (Standard dev.)0.00011638759 (±0.010289645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66834_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66834_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BAM-SurA complex (P2-visible 1)

EntireName: BAM-SurA complex (P2-visible 1)
Components
  • Complex: BAM-SurA complex (P2-visible 1)
    • Complex: BAM complex
      • Protein or peptide: Outer membrane protein assembly factor BamA
      • Protein or peptide: Outer membrane protein assembly factor BamB
      • Protein or peptide: Outer membrane protein assembly factor BamC
      • Protein or peptide: Outer membrane protein assembly factor BamD
      • Protein or peptide: Outer membrane protein assembly factor BamE
    • Complex: Chaperone SurA
      • Protein or peptide: Chaperone SurA

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Supramolecule #1: BAM-SurA complex (P2-visible 1)

SupramoleculeName: BAM-SurA complex (P2-visible 1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: BAM complex

SupramoleculeName: BAM complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Chaperone SurA

SupramoleculeName: Chaperone SurA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 90.62732 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV ...String:
MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV FQEGVSAEIQ QINIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NI DSTQVSL TPDKKGIYVT VNITEGDQYK LSGVEVCGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYP RVQSMP EINDADKTVK LRVNVDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDT DTQRV PGSPDQVDVV YKVKERNTGS FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTV DGVS LGGRLFYNDF QADDADLSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSD QDN SFKTDDFTFN YGWTYNKLDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDG LG GKEMPFYENF YAGGSSTVRG FQSNTIGPKA VYFPHQASNY DPDYDYESAT QDGAKDLSKS DDAVGGNAMA VASLEFIT P TPFISDKYAN SVRTSFFWDM GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAE QFQFNIGKTW

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.918945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN ...String:
MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN GQLQALNEAD GAVKWTVNLD MPSLSLRGES APTTAFGAAV VGGDNGRVSA VLMEQGQMIW QQRISQATGS TE IDRLSDV DTTPVVVNGV VFALAYNGNL TALDLRSGQI MWKRELGSVN DFIVDGNRIY LVDQNDRVMA LTIDGGVTLW TQS DLLHRL LTSPVLYNGN LVVGDSEGYL HWINVEDGRF VAQQKVDSSG FQTEPVAADG KLLIQAKDGT VYSITR

UniProtKB: Outer membrane protein assembly factor BamB

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Macromolecule #3: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.875277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ ...String:
MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ GYQQAVTVKL LNLEQAGKPV ADAASMQRYS TEMMNVISAG LDKSATDAAN AAQNRASTTM DVQSAADDTG LP MLVVRGP FNVVWQRLPA ALEKVGMKVT DSTRSQGNMA VTYKPLSDSD WQELGASDPG LASGDYKLQV GDLDNRSSLQ FID PKGHTL TQSQNDALVA VFQAAFSK

UniProtKB: Outer membrane protein assembly factor BamC

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Macromolecule #4: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.85835 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV ...String:
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV FLKDRLAKYE YSVAEYYTER GAWVAVVNRV EGMLRDYPDT QATRDALPLM ENAYRQMQMN AQAEKVAKII AA NSSNT

UniProtKB: Outer membrane protein assembly factor BamD

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Macromolecule #5: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.310977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGN

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #6: Chaperone SurA

MacromoleculeName: Chaperone SurA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.781176 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKNWKTLLL GIAMIANTSF AAPQVVDKVA AVVNNGVVLE SDVDGLMQSV KLNAAQARQQ LPDDATLRHQ IMERLIMDQI ILQMGQKMG VKISDEQLDQ AIANIAKQNN MTLDQMRSRL AYDGLNYNTY RNQIRKEMII SEVRNNEVRR RITILPQEVE S LAQQVGNQ ...String:
MAKNWKTLLL GIAMIANTSF AAPQVVDKVA AVVNNGVVLE SDVDGLMQSV KLNAAQARQQ LPDDATLRHQ IMERLIMDQI ILQMGQKMG VKISDEQLDQ AIANIAKQNN MTLDQMRSRL AYDGLNYNTY RNQIRKEMII SEVRNNEVRR RITILPQEVE S LAQQVGNQ NDASTELNLS HILIPLPENP TSDQVNEAES QARAIVDQAR NGADFGKLAI AHSADQQALN GGQMGWGRIQ EL PGIFAQA LSTAKKGDIV GPIRSGVGFH ILKVNDLRGE SKNISVTEVH ARHILLKPSP IMTDEQARVK LEQIAADIKS GKT TFAAAA KEFSQDPGSA CQGGDLGWAT PDIFDPAFRD ALTRLNKGQM SAPVHSSFGW HLIELLDTRN VDKTDAAQKD RAYR MLMNR KFSEEAASWM QEQRASAYVK ILSNHHHHHH HHHH

UniProtKB: Chaperone SurA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 232210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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