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- EMDB-45756: The cryo-EM structure of BamAD subcomplex from Neisseria gonorrhoeae -

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Basic information

Entry
Database: EMDB / ID: EMD-45756
TitleThe cryo-EM structure of BamAD subcomplex from Neisseria gonorrhoeae
Map data
Sample
  • Complex: NgBamAD
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamD
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 / protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane
Similarity search - Function
Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / 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) ...Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / 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 BamD / Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 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_45756.png

Downloads & links

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Map

FileDownload / File: emd_45756.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

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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-0.73488414 - 1.3889148
Average (Standard dev.)0.0022923667 (±0.041449178)
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: #1

Fileemd_45756_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45756_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 : NgBamAD

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

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Supramolecule #1: NgBamAD

SupramoleculeName: NgBamAD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Structure of NgBamAD generated from a subclass of our NgBamACDE dataset.
Source (natural)Organism: Neisseria gonorrhoeae (bacteria) / Strain: FA1090
Molecular weightTheoretical: 114 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 signal sequence from Neisseria gonorrhoeae BamA was replaced with the pelB localization 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 signal from E. coli BamB
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria) / Strain: FA1090
Molecular weightTheoretical: 31.535693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLRKLLLPG LLSVTLLSGC AMGATQGTAD KDAQITQDWS VEKLYAEAQD ELNSSNYTRA VKLYEILESR FPTSRHARQS QLDTAYAYY KDDEKDKALA AIERFRRLHP QHPNMDYALY LRGLVLFNED QSFLNKLASQ DWSDRDPKAN REAYQAFAEL V QRFPNSKY ...String:
MQLRKLLLPG LLSVTLLSGC AMGATQGTAD KDAQITQDWS VEKLYAEAQD ELNSSNYTRA VKLYEILESR FPTSRHARQS QLDTAYAYY KDDEKDKALA AIERFRRLHP QHPNMDYALY LRGLVLFNED QSFLNKLASQ DWSDRDPKAN REAYQAFAEL V QRFPNSKY AADATARMVK LVDALGGNEM SVARYYMKRG AYIAAANRAK KIIGSYQNTR YVEESLAILE LAYKKLDKPQ LA ADTRRVL ETNFPKSPFL THAWQPDDMP WWRYWH

UniProtKB: Outer membrane protein assembly factor BamD

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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 / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 35335
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
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9cn1:
The cryo-EM structure of BamAD subcomplex from Neisseria gonorrhoeae

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