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- EMDB-49679: Pseudomonas aeruginosa CdrA N*-terminal domain plus ~6 repeats of... -

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Basic information

Entry
Database: EMDB / ID: EMD-49679
TitlePseudomonas aeruginosa CdrA N*-terminal domain plus ~6 repeats of the extension domain
Map dataCdrA N*-terminal domain with about six repeats of the extension domain
Sample
  • Complex: N*-terminal domain of CdrA plus ~6 repeats of the extension domain
    • Protein or peptide: CdrA N*-terminal domain plus ~6 repeats of the extension domain
Keywordsfibrillar adhesin / putative adhesive domain / Pseudomonas aeruginosa / CdrA / extension domain / CELL ADHESION
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 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_49679.png

Downloads & links

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Map

FileDownload / File: emd_49679.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCdrA N*-terminal domain with about six repeats of the extension domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 512 pix.
= 606.208 Å		1.18 Å/pix.
x 512 pix.
= 606.208 Å		1.18 Å/pix.
x 512 pix.
= 606.208 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: 0.75
Minimum - Maximum-0.47783905 - 3.0710769
Average (Standard dev.)-0.00000793376 (±0.024237532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 606.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CdrA N*-terminal domain with about six repeats of...

Fileemd_49679_half_map_1.map
AnnotationCdrA N*-terminal domain with about six repeats of the extension domain half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CdrA N*-terminal domain with about six repeats of...

Fileemd_49679_half_map_2.map
AnnotationCdrA N*-terminal domain with about six repeats of the extension domain half map B
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 plus ~6 repeats of the extension domain

EntireName: N*-terminal domain of CdrA plus ~6 repeats of the extension domain
Components
  • Complex: N*-terminal domain of CdrA plus ~6 repeats of the extension domain
    • Protein or peptide: CdrA N*-terminal domain plus ~6 repeats of the extension domain

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Supramolecule #1: N*-terminal domain of CdrA plus ~6 repeats of the extension domain

SupramoleculeName: N*-terminal domain of CdrA plus ~6 repeats of the extension domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 167 KDa

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Macromolecule #1: CdrA N*-terminal domain plus ~6 repeats of the extension domain

MacromoleculeName: CdrA N*-terminal domain plus ~6 repeats of the extension domain
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
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 TPAQLIVSAD AKTKVYGDAD PTLTYQVSGL KNSDTAAGVL SGNLGRVAGE NVGNYGILQG GLGLNTANYT LSYVGNDLRI TPAQLNVIAD AKTKVYGDLD PALTYQVSGL KRGDTAGAVL NGGSLSRVAG ENVGVYGINQ GGLGLVSSNY TLNYQGNNLT ITKALLNVIA DAKTKVYGDA DPALTYQVSG LKNGDTAGAV LNGGSLSRVA GENVGVYGIN QGGLGLLSAN YDLSYQGNNL TITKALLNVI ADAKTKVYGD ADPSLTYQVS GLKNGDTAGS ILTGGLNRAA GENVGVYGIN QGDLALNSGN YDLSYQGNNL TITKALLNVI ADAKTKVYGD ADPSLTYQVS GLKNGDTAGA VLNGGGLVRV SGENVGNYAI QQGGLGLVSG NYDLAYQGNN LTITKALLNV IADAKTKVYG DADPSLTYQV SGLKNGDSAG SILTGGLNRA AGENVGVYGI NQGDLALNSG NYDLSYQGNN LTIT

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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 plus part of the extension 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: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 9017
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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