[English] 日本語
Yorodumi
- EMDB-43835: Structure of biofilm-forming functional amyloid PSMa1 from Staphy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43835
TitleStructure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus
Map dataDeepEM processed map.
Sample
  • Complex: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
    • Protein or peptide: Phenol-soluble modulin alpha 1 peptide
Keywordsfunctional amyloid fibril / biofilm / bacterial biofilm / phenol soluble modulin alpha1 / PSMa1 / STRUCTURAL PROTEIN
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 1 peptide
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHansen KH / Byeon CH / Liu Q / Drace T / Boesen T / Conway JF / Andreasen M / Akbey U
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proceedings of the National Academy of Sciences of the United States of America
Year: 2024
Title: Structure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus
Authors: Hansen KH / Byeon CH / Liu Q / Drace T / Boesen T / Conway JF / Andreasen M / Akbey U
History
DepositionFeb 27, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43835.png

Downloads & links

-
Map

FileDownload / File: emd_43835.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEM processed map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 194.1 Å		0.65 Å/pix.
x 300 pix.
= 194.1 Å		0.65 Å/pix.
x 300 pix.
= 194.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.000914374 - 1.7745667
Average (Standard dev.)0.0134513 (±0.08805764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 194.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_43835_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: CryoSparc output unsharpened.

Fileemd_43835_additional_1.map
AnnotationCryoSparc output unsharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: CryoSparc sharpened to B:-100

Fileemd_43835_additional_2.map
AnnotationCryoSparc sharpened to B:-100
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: CryoSparc auto-sharpened

Fileemd_43835_additional_3.map
AnnotationCryoSparc auto-sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B from CryoSparc

Fileemd_43835_half_map_1.map
AnnotationHalf Map B from CryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A from CryoSparc

Fileemd_43835_half_map_2.map
AnnotationHalf Map A from CryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)

EntireName: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
Components
  • Complex: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
    • Protein or peptide: Phenol-soluble modulin alpha 1 peptide

-
Supramolecule #1: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)

SupramoleculeName: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Biofilm forming functional amyloid from Staphylococcus aureus PSMa1 is produced by peptide-synthesis
Source (natural)Organism: Staphylococcus aureus (bacteria)

-
Macromolecule #1: Phenol-soluble modulin alpha 1 peptide

MacromoleculeName: Phenol-soluble modulin alpha 1 peptide / type: protein_or_peptide / ID: 1 / Number of copies: 64 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 2.262817 KDa
SequenceString:
MGIIAGIIKV IKSLIEQFTG K

UniProtKB: Phenol-soluble modulin alpha 1 peptide

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.8 / Details: water
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
Details: C-Flat R2/2 Cu 300 mesh holey carbon grids (Protochips) were glow discharged for 45 s at 15 mA using a Quorum GloQube Plus
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: plunge-frozen in liquid ethane using a Vitrobot Mark IV plunge freezer with a blot force of zero at 4C and 99% humidity..
Details3 microL of PSMa1 (0.5 mg/mL) was applied to grids Blotted for 6s

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3002 / Average exposure time: 1.5 sec. / Average electron dose: 63.0 e/Å2
Details: A total of 3,002 movies of the PSMa1 sample were collected
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 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

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.95 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.578 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1)
Details: The overall resolution estimated by CryoSPARC was 3.51A according to the gold standard Fourier shell correlation cutoff at 0.143. The final map was sharpened by using DeepEMhancer
Number images used: 100
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT / Overall B value: 50
Output model

PDB-9atw:
Structure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus

+
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://pdbjlvh1.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