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- EMDB-49677: Pseudomonas aeruginosa CdrA N*-terminal domain -

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Basic information

Entry
Database: EMDB / ID: EMD-49677
TitlePseudomonas aeruginosa CdrA N*-terminal domain
Map dataPseudomonas aeruginosa CdrA N*-terminal domain
Sample
  • Complex: N*-terminal domain of CdrA
    • Protein or peptide: CdrA
Keywordsfibrillar adhesin / putative adhesive domain / P. aeruginosa / CdrA / CELL ADHESION
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsFazio NT / Reichhardt C / di Trani JM / Moss E / Barrington M / Davidson C / Jaysingh AM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM155188 United States
CitationJournal: Commun Biol / Year: 2026
Title: Structure of the Pseudomonas aeruginosa fibrillar adhesin CdrA reveals a clawlike domain and modular repeats
Authors: Fazio NT / Moss E / Barrington MJ / BoClair M / Jaysingh A / Di Trani J / Reichhardt C
History
DepositionMar 13, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49677.png

Downloads & links

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Map

FileDownload / File: emd_49677.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudomonas aeruginosa CdrA N*-terminal domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 303.104 Å		1.18 Å/pix.
x 256 pix.
= 303.104 Å		1.18 Å/pix.
x 256 pix.
= 303.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.184 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.1052371 - 0.4970735
Average (Standard dev.)0.0005773824 (±0.023352696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 303.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Pseudomonas aeruginosa CdrA N*-terminal domain - half map B

Fileemd_49677_half_map_1.map
AnnotationPseudomonas aeruginosa CdrA N*-terminal domain - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pseudomonas aeruginosa CdrA N*-terminal domain - half map A

Fileemd_49677_half_map_2.map
AnnotationPseudomonas aeruginosa CdrA N*-terminal domain - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : N*-terminal domain of CdrA

EntireName: N*-terminal domain of CdrA
Components
  • Complex: N*-terminal domain of CdrA
    • Protein or peptide: CdrA

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Supramolecule #1: N*-terminal domain of CdrA

SupramoleculeName: N*-terminal domain of CdrA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 167 KDa

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Macromolecule #1: CdrA

MacromoleculeName: CdrA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: PTTLRIVASG GTSGSVGGAN GASGDATVNA SVVTGALAGG KVTLSASDRL SVEAPLITSN LGGASRGLEL IATGPAGAVD ISAPILFRNG SLAIRAGGNI NFLSGGTPQT SGIVDLGSGT LWMQTSTAGK ISQQAGTALI AANLAGRAGS IDLASWDNYA GNLALQTFNG ...String:
PTTLRIVASG GTSGSVGGAN GASGDATVNA SVVTGALAGG KVTLSASDRL SVEAPLITSN LGGASRGLEL IATGPAGAVD ISAPILFRNG SLAIRAGGNI NFLSGGTPQT SGIVDLGSGT LWMQTSTAGK ISQQAGTALI AANLAGRAGS IDLASWDNYA GNLALQTFNG TLKYRQSNAT GVTTSGTVFD PFINQSMTGT AQNIVSSVGT RILEANSVGT TGNYTLTADG NSEFDRLVFT ALPYRRVSGS ASFPTNDSSD YLVTNLRYQV NGSNVTATPN GGAPSGFTVA AGNGSVTTWT GNWGTSWGVK GFGGVIGVTD ELQYDVGTGL TEELIFGLGG KTSRVDTRLD LFMREGAFNS FAERAQVEMF KTTTTAGDIL SRQQTATLTA NDATRVYGDV NPTLTATMSG INAIDAYVNS QFNDLYQATA STTATQASNV GQYAITGNAN GSEYFSQRYQ LVRQDGRLTV T

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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

Concentration0.08 mg/mL
BufferpH: 6.7
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
20.0 mM3-(N-morpholino)propanesulfonic acid
VitrificationCryogen name: NITROGEN
DetailsThis sample was purified full-length protein, but only the N*-terminal domain was selected as the particle.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 82.0 K / Max: 84.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 5.94 sec. / Average electron dose: 1.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
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: 3505729
CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 51297
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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