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- EMDB-67046: pilus-like-beta, a bacteria pilus-like structure obtained from a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-67046
Titlepilus-like-beta, a bacteria pilus-like structure obtained from a Karst cave from Guilin City, Guangxi Zhuang Autonomous Region, China
Map data
Sample
  • Complex: dropping water from a Karst cave from Guilin City, Guangxi Province, China
    • Protein or peptide: Bacteria pilus (like)
KeywordsBacteria Pilus / PROTEIN FIBRIL
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsHu MX / Zhang Q / Chen S / Ge QJ / Wang JW / Yan N / Qin LJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254, 32171190, 92478205 China
CitationJournal: To Be Published
Title: Absolute hand determination of glycofibrils from natural sources in cryo-EM
Authors: Zhang Q / Qin LJ / Wang TT / Li ZQ / Zhang YL / Chen S / Ge QJ / Yan N / Wang JW / Hu MX
History
DepositionNov 12, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67046.png

Downloads & links

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Map

FileDownload / File: emd_67046.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 380 pix.
= 352.26 Å		0.93 Å/pix.
x 380 pix.
= 352.26 Å		0.93 Å/pix.
x 380 pix.
= 352.26 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.927 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.55555606 - 1.0299344
Average (Standard dev.)0.0016412684 (±0.030810138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 352.26 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_67046_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67046_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 : dropping water from a Karst cave from Guilin City, Guangxi Provin...

EntireName: dropping water from a Karst cave from Guilin City, Guangxi Province, China
Components
  • Complex: dropping water from a Karst cave from Guilin City, Guangxi Province, China
    • Protein or peptide: Bacteria pilus (like)

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Supramolecule #1: dropping water from a Karst cave from Guilin City, Guangxi Provin...

SupramoleculeName: dropping water from a Karst cave from Guilin City, Guangxi Province, China
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unidentified (others)

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Macromolecule #1: Bacteria pilus (like)

MacromoleculeName: Bacteria pilus (like) / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 16.735275 KDa
SequenceString:
GTTLISLMIV VAIIGILAAV ALPAYQDYTV RARVTEGLAL AGDLIYMTAG AAADAALGSV VATWNAQSGA GLGAKSKYVT SILATMASG LITITYIADT VGLGAAENTL TLTPMVLTDG AGQALAAAQG AGMTGVIDWA CASALNATAT AHGIAGAAVG T LQSKFAPA LCR

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 100.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 10.08 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12518
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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