[English] 日本語
Yorodumi
- PDB-9nqd: Structural Basis of Pseudomonas FapC Biofilm-Forming Functional A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nqd
TitleStructural Basis of Pseudomonas FapC Biofilm-Forming Functional Amyloid Formation
ComponentsFunctional amyloid subunit FapC
KeywordsSTRUCTURAL PROTEIN / FapC Functional Amyloid Pseudomonas C / AMYLOID / FIBRIL / BIOFILM / FUNCTIONAL AMYLOID
Function / homologypilus / cell adhesion / extracellular region / Functional amyloid subunit FapC
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHansen, K.H. / Golcuk, M. / Byeon, C.B. / Plechinger, E.B. / Conway, J.F. / Andreasen, M. / Gur, M. / Akbey, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Basis of Pseudomonas FapC Biofilm-Forming Functional Amyloid Formation
Authors: Hansen, K.H. / Golcuk, M. / Byeon, C.B. / Plechinger, E.B. / Conway, J.F. / Andreasen, M. / Gur, M. / Akbey, U.
History
DepositionMar 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
3: Functional amyloid subunit FapC
4: Functional amyloid subunit FapC
5: Functional amyloid subunit FapC
6: Functional amyloid subunit FapC
7: Functional amyloid subunit FapC
8: Functional amyloid subunit FapC
9: Functional amyloid subunit FapC
0: Functional amyloid subunit FapC
AA: Functional amyloid subunit FapC
AB: Functional amyloid subunit FapC
AC: Functional amyloid subunit FapC
AD: Functional amyloid subunit FapC


Theoretical massNumber of molelcules
Total (without water)270,89112
Polymers270,89112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Functional amyloid subunit FapC / Amyloid-like fimbrin subunit FapC / ALF subunit FapC / Fibril amyloid subunit FapC


Mass: 22574.234 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: FapC 25-250, without signal peptide (1-24). / Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: UK4 / Gene: fapC, HZ99_04090, PSUK4_00030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DXF5
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: FapC / Type: COMPLEX
Details: FapC. Residue between 25-250, without signal peptide. Additional methionine on the N-terminus and a histidine purification tag of LEHHHHHH at the C-terminus.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 23.755 kDa/nm / Experimental value: YES
Source (natural)Organism: Pseudomonas fluorescens (bacteria) / Strain: UK4
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 0.2 mili Bar / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 295 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 91 K / Temperature (min): 87 K
Image recordingAverage exposure time: 4.8 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8870
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansSampling size: 15 µm / Width: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5particle selection
2EPU3.2image acquisitionTFS
4cryoSPARC4.5CTF correction
7UCSF ChimeraX1.8model fitting
9UCSF ChimeraX1.8initial Euler assignment
10UCSF ChimeraX1.8final Euler assignment
11cryoSPARC4.5classification
12cryoSPARC4.53D reconstruction
13UCSF ChimeraX1.8model refinement
14PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.266 ° / Axial rise/subunit: 14.562 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 762000
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71848 / Details: Determined by CryoSPARC 4.5. / Symmetry type: HELICAL
Atomic model buildingB value: 15.3 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingAccession code: C4IN70 / Chain residue range: 25-250 / Source name: AlphaFold / Type: in silico model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more