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- EMDB-50954: Cryo-EM map of the type 1 chaperone-usher pilus FimD-tip complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50954
TitleCryo-EM map of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2
Map dataMap of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2 (sharpened)
Sample
  • Complex: FimDHGFAnC
    • Protein or peptide: Outer membrane usher protein FimD
    • Protein or peptide: Chaperone protein FimC
Keywordschaperone / usher / pilus / tip / MEMBRANE PROTEIN
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / : / protein folding chaperone / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. ...Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer membrane usher protein FimD / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBachmann P / Afanasyev P / Boehringer D / Glockshuber R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_201234 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM map of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2
Authors: Bachmann P / Afanasyev P / Boehringer D / Glockshuber R
History
DepositionJul 9, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50954.png

Downloads & links

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Map

FileDownload / File: emd_50954.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2 (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 300 pix.
= 388.8 Å		1.3 Å/pix.
x 300 pix.
= 388.8 Å		1.3 Å/pix.
x 300 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.8610887 - 1.3058333
Average (Standard dev.)-0.0005149079 (±0.014744399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 388.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 chaperone-usher pilus FimD-tip...

Fileemd_50954_additional_1.map
AnnotationMap of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2 (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of the type 1 chaperone-usher pilus...

Fileemd_50954_half_map_1.map
AnnotationHalf-map B of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of the type 1 chaperone-usher pilus...

Fileemd_50954_half_map_2.map
AnnotationHalf-map A of the type 1 chaperone-usher pilus FimD-tip complex - Conformer 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnC

EntireName: FimDHGFAnC
Components
  • Complex: FimDHGFAnC
    • Protein or peptide: Outer membrane usher protein FimD
    • Protein or peptide: Chaperone protein FimC

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Supramolecule #1: FimDHGFAnC

SupramoleculeName: FimDHGFAnC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane usher protein FimD

MacromoleculeName: Outer membrane usher protein FimD / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLYFNPRFLA DDPQAVADLS RFENGQELPP GTYRVDIYLN NGYMATRDVT FNTGDSEQGI VPCLTRAQLA SMGLNTASVA GMNLLADDAC VPLTTMVQDA TAHLDVGQQR LNLTIPQAFM SNRARGYIPP ELWDPGINAG LLNYNFSGNS VQNRIGGNSH YAYLNLQSGL ...String:
DLYFNPRFLA DDPQAVADLS RFENGQELPP GTYRVDIYLN NGYMATRDVT FNTGDSEQGI VPCLTRAQLA SMGLNTASVA GMNLLADDAC VPLTTMVQDA TAHLDVGQQR LNLTIPQAFM SNRARGYIPP ELWDPGINAG LLNYNFSGNS VQNRIGGNSH YAYLNLQSGL NIGAWRLRDN TTWSYNSSDR SSGSKNKWQH INTWLERDII PLRSRLTLGD GYTQGDIFDG INFRGAQLAS DDNMLPDSQR GFAPVIHGIA RGTAQVTIKQ NGYDIYNSTV PPGPFTINDI YAAGNSGDLQ VTIKEADGST QIFTVPYSSV PLLQREGHTR YSITAGEYRS GNAQQEKPRF FQSTLLHGLP AGWTIYGGTQ LADRYRAFNF GIGKNMGALG ALSVDMTQAN STLPDDSQHD GQSVRFLYNK SLNESGTNIQ LVGYRYSTSG YFNFADTTYS RMNGYNIETQ DGVIQVKPKF TDYYNLAYNK RGKLQLTVTQ QLGRTSTLYL SGSHQTYWGT SNVDEQFQAG LNTAFEDINW TLSYSLTKNA WQKGRDQMLA LNVNIPFSHW LRSDSKSQWR HASASYSMSH DLNGRMTNLA GVYGTLLEDN NLSYSVQTGY AGGGDGNSGS TGYATLNYRG GYGNANIGYS HSDDIKQLYY GVSGGVLAHA NGVTLGQPLN DTVVLVKAPG AKDAKVENQT GVRTDWRGYA VLPYATEYRE NRVALDTNTL ADNVDLDNAV ANVVPTRGAI VRAEFKARVG IKLLMTLTHN NKPLPFGAMV TSESSQSSGI VADNGQVYLS GMPLAGKVQV KWGEEENAHC VANYQLPPES QQQLLTQLSA ECRLVPRGSW SHPQFEK

UniProtKB: Outer membrane usher protein FimD

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Macromolecule #2: Chaperone protein FimC

MacromoleculeName: Chaperone protein FimC / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVALGATRV IYPAGQKQEQ LAVTNNDENS TYLIQSWVEN ADGVKDGRFI VTPPLFAMKG KKENTLRILD ATNNQLPQDR ESLFWMNVKA IPSMDKSKLT ENTLQLAIIS RIKLYYRPAK LALPPDQAAE KLRFRRSANS LTLINPTPYY LTVTELNAGT RVLENALVPP ...String:
MGVALGATRV IYPAGQKQEQ LAVTNNDENS TYLIQSWVEN ADGVKDGRFI VTPPLFAMKG KKENTLRILD ATNNQLPQDR ESLFWMNVKA IPSMDKSKLT ENTLQLAIIS RIKLYYRPAK LALPPDQAAE KLRFRRSANS LTLINPTPYY LTVTELNAGT RVLENALVPP MGESTVKLPS DAGSNITYRT INDYGALTPK MTGVME

UniProtKB: Chaperone protein FimC

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.1 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 98487
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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