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- EMDB-45755: The cryo-EM structure of BamADE subcomplex from Neisseria gonorrhoeae -

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Basic information

Entry
Database: EMDB / ID: EMD-45755
TitleThe cryo-EM structure of BamADE subcomplex from Neisseria gonorrhoeae
Map data
Sample
  • Complex: NgBamADE
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamE
Keywordsbeta barrel assembly machinery / BAM complex / outer membrane protein / Neisseria / Neisseria gonnorhoeae / protein folding / beta barrel membrane protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


establishment of competence for transformation / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity
Similarity search - Function
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 / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat ...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 / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsBillings EM / Noinaj N
Funding support United States, 5 items
OrganizationGrant numberCountry
American Heart Association909066 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132024 United States
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129539 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127884 United States
CitationJournal: Structure / Year: 2025
Title: Structural insights into outer membrane protein biogenesis in pathogenic Neisseria.
Authors: Evan Billings / Zixing Fan / Moloud Aflaki Sooreshjani / James C Gumbart / Nicholas Noinaj /
Abstract: N. gonorrhoeae (Ngo) causes the sexually transmitted infection gonorrhea with ∼106 million infections worldwide annually. Ngo infections can result in an increased risk of acquiring HIV, ...N. gonorrhoeae (Ngo) causes the sexually transmitted infection gonorrhea with ∼106 million infections worldwide annually. Ngo infections can result in an increased risk of acquiring HIV, infertility, and blindness. To combat Ngo infections, we report the cryoelectron microscopy (cryo-EM) structure of the Ngo β-barrel assembly machinery (NgBAM), which is responsible for the biogenesis of β-barrel outer membrane proteins (OMPs). NgBAM was observed in an inward-open state; however, the polypeptide transport-associated (POTRA) domains more closely match those found in the outward-open state in E. coli β-barrel assembly machinery (BAM). The barrel seam of NgBamA consists of partial pairing of strand β1 with β16; no outward-open state of NgBAM was observed. Molecular dynamics (MD) simulations reveal unique overall dynamics and interplay between the POTRA domains of NgBamA and NgBamD. We propose that in Ngo, initial recognition occurs in the inward-open state where the last strand of the OMP partially pairs with β1 of NgBamA and must compete off β16.
History
DepositionJul 15, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45755.png

Downloads & links

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Map

FileDownload / File: emd_45755.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.664 Å		1.07 Å/pix.
x 256 pix.
= 273.664 Å		1.07 Å/pix.
x 256 pix.
= 273.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.069 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.899881 - 1.7661715
Average (Standard dev.)0.0030045619 (±0.046158615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45755_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_45755_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NgBamADE

EntireName: NgBamADE
Components
  • Complex: NgBamADE
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamE

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Supramolecule #1: NgBamADE

SupramoleculeName: NgBamADE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Structure of NgBamADE generated from a subclass of our NgBamACDE dataset.
Source (natural)Organism: Neisseria gonorrhoeae (bacteria) / Strain: FA1090
Molecular weightTheoretical: 128 kDa/nm

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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
Details: The endogenous BamA signal sequence was replaced with the pelB signal sequence.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria) / Strain: FA1090
Molecular weightTheoretical: 88.025969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKYLLPTAA AGLLLLAAQP AMDFTIQDIR VEGLQRTEPS TVFNYLPVKV GDTYNDTHGS AIIKSLYATG FFDDVRVETA DGQLLLTVI ERPTIGSLNI TGAKMLQNDA IKKNLESFGL AQSQYFNQAT LNQAVAGLKE EYLGRGKLNI QITPKVTKLA R NRVDIDIT ...String:
MGKYLLPTAA AGLLLLAAQP AMDFTIQDIR VEGLQRTEPS TVFNYLPVKV GDTYNDTHGS AIIKSLYATG FFDDVRVETA DGQLLLTVI ERPTIGSLNI TGAKMLQNDA IKKNLESFGL AQSQYFNQAT LNQAVAGLKE EYLGRGKLNI QITPKVTKLA R NRVDIDIT IDEGKSAKIT DIEFEGNQVY SDRKLMRQMS LTEGGIWTWL TRSDRFDRQK FAQDMEKVTD FYQNNGYFDF RI LDTDIQT NEDKTRQTIK ITVHEGGRFR WGKVSIEGDT NEVPKAELEK LLTMKPGKWY ERQQMTAVLG EIQNRMGSAG YAY SEISVQ PLPNAGTKTV DFVLHIEPGR KIYVNEIHIT GNNKTRDEVV RRELRQMESA PYDTSKLQRS KERVELLGYF DNVQ FDAVP LAGTPDKVDL NMSLTERSTG SLDLSAGWVQ DTGLVMSAGV SQDNLFGTGK SAALRASRSK TTLNGSLSFT DPYFT ADGV SLGYDIYGKA FDPRKASTSV KQYKTTTAGG GVRMGIPVTE YDRVNFGLAA EHLTVNTYNK APKRYADFIR KYGKTD GAD GSFKGLLYKG TVGWGRNKTD SASWPTRGYL TGVNAEIALP GSKLQYYSAT HNQTWFFPLS KTFTLMLGGE VGIAGGY GR TKEIPFFENF YGGGLGSVRG YESGTLGPKV YDEYGEKISY GGNKKANVSA ELLFPMPGAK DARTVRLSLF ADAGSVWD G RTYTAAENGN NKSVYSENAH KSTFTNELRY SAGGAVTWLS PLGPMKFSYA YPLKKKPEDE IQRFQFQLGT TF

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 2
Details: The endogenous lipidation signal sequence was replaced with the lipidation sequence from E. coli BamB.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria) / Strain: FA1090
Molecular weightTheoretical: 31.334385 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKYLLPTAA AGLLLLAAQP AMATQGTADK DAQITQDWSV EKLYAEAQDE LNSSNYTRAV KLYEILESRF PTSRHARQSQ LDTAYAYYK DDEKDKALAA IERFRRLHPQ HPNMDYALYL RGLVLFNEDQ SFLNKLASQD WSDRDPKANR EAYQAFAELV Q RFPNSKYA ...String:
MGKYLLPTAA AGLLLLAAQP AMATQGTADK DAQITQDWSV EKLYAEAQDE LNSSNYTRAV KLYEILESRF PTSRHARQSQ LDTAYAYYK DDEKDKALAA IERFRRLHPQ HPNMDYALYL RGLVLFNEDQ SFLNKLASQD WSDRDPKANR EAYQAFAELV Q RFPNSKYA ADATARMVKL VDALGGNEMS VARYYMKRGA YIAAANRAKK IIGSYQNTRY VEESLAILEL AYKKLDKPQL AA DTRRVLE TNFPKSPFLT HAWQPDDMPW WRYWH

UniProtKB: Outer membrane protein assembly factor BamD

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Macromolecule #3: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 3
Details: The endogenous lipidation signal sequence was replaced with the lipidation signal from E. coli BamB. The C-terminus contains a 10x histidine tag.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria) / Strain: FA1090
Molecular weightTheoretical: 15.915229 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQLRKLLLPG LLSVTLLSGC AMDSVERVSL FPSYKLKIIQ GNELEPRAVA ALRPGMTKDQ VLLLLGSPIL RDAFHTDRWD YTFNTSRNG IIKERSNLTV YFENGVLVRT EGDALQNAAE ALRAKQNADK QHHHHHHHHH H

UniProtKB: Outer membrane protein assembly factor BamE

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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

Concentration4.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4sodium phosphate
1.8 mMKH2PO4potassium phosphate
0.01 %LMNGlauryl maltose neopentyl glycol

Details: 1xPBS pH 7.5, with 0.01% LMNG
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force of 2, blot time of 15 seconds..
DetailsSample used directly after purification over a Superdex200 size exclusion chromatography column.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 10825 / Average exposure time: 0.03 sec. / Average electron dose: 41.87 e/Å2
Details: Data was collected at the National Center for Cryo-EM Access and Training, using one of the Titan Krios (Elizabeth).
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 9.700000000000001 µm / Nominal defocus min: 2.23 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4552267
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2) / Software - details: patch motion and CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4k3b

Final reconstructionNumber classes used: 3 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 27691
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 3 / Avg.num./class: 90000 / Software - Name: cryoSPARC (ver. 3.2)

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Atomic model buiding 1

Initial model
PDB IDChain

4k3b

chain_id: A, source_name: PDB, initial_model_type: experimental model

5waq

chain_id: A, source_name: PDB, initial_model_type: experimental model

5wam

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9cn0:
The cryo-EM structure of BamADE subcomplex from Neisseria gonorrhoeae

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