[English] 日本語
Yorodumi
- EMDB-41442: Acinetobacter GP16 Type IV pilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41442
TitleAcinetobacter GP16 Type IV pilus
Map datamap
Sample
  • Complex: Acinetobacter genomosp.16 Tyoe IV pilus
    • Protein or peptide: Fimbrial protein
    • Protein or peptide: Fimbrial protein
KeywordsT4P / Competence / CELL ADHESION
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesAcinetobacter genomosp. 16BJ (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsMeng R / Xing Z / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01GM141659 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of Acinetobacter type IV pili targeting by an RNA virus.
Authors: Ran Meng / Zhongliang Xing / Jeng-Yih Chang / Zihao Yu / Jirapat Thongchol / Wen Xiao / Yuhang Wang / Karthik Chamakura / Zhiqi Zeng / Fengbin Wang / Ry Young / Lanying Zeng / Junjie Zhang /
Abstract: Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. ...Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into the interaction between Acinetobacter phage AP205 and type IV pili. Using cryo-electron microscopy, we solve structures of the AP205 virion with an asymmetric dimer of maturation proteins, the native Acinetobacter type IV pili bearing a distinct post-translational pilin cleavage, and the pili-bound AP205 showing its maturation proteins adapted to pilin modifications, allowing each phage to bind to one or two pili. Leveraging these results, we develop a 20-kilodalton AP205-derived protein scaffold targeting type IV pili in situ, with potential for research and diagnostics.
History
DepositionAug 3, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41442.png

Downloads & links

-
Map

FileDownload / File: emd_41442.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08914391 - 0.28763655
Average (Standard dev.)0.00016636743 (±0.010421797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: A

Fileemd_41442_half_map_1.map
AnnotationA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: B

Fileemd_41442_half_map_2.map
AnnotationB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Acinetobacter genomosp.16 Tyoe IV pilus

EntireName: Acinetobacter genomosp.16 Tyoe IV pilus
Components
  • Complex: Acinetobacter genomosp.16 Tyoe IV pilus
    • Protein or peptide: Fimbrial protein
    • Protein or peptide: Fimbrial protein

-
Supramolecule #1: Acinetobacter genomosp.16 Tyoe IV pilus

SupramoleculeName: Acinetobacter genomosp.16 Tyoe IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filamentous Type IV pilus
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 11 kDa/nm

-
Macromolecule #1: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 7.470747 KDa
SequenceString:
TLIELMIVVA IIGILAAIAI PQYQNYIAKS QVSRVMSETG SLKTVIETCI LDGKTAANCE LGWTNSNLLG

UniProtKB: Fimbrial protein

-
Macromolecule #2: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 6.999778 KDa
SequenceString:
STAAVTGQTG LTITYPASAT ESAAIQGTFG NSAAIKIKNQ TLTWTRTPEG AWSCATTVEA KFKPAGCAS

UniProtKB: Fimbrial protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris (hydroxymethyl) aminomethane (THAM) hydrochloride
200.0 mMNaClSodium Chloride

Details: 20mM Tris-HCl, 200mM NaCl, pH 8.0
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: 3uL sample applied to a QuantiFoil R2/1 grid.
Detailsvitreous Typy IV pilus

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 135000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 92 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 900000
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-8tob:
Acinetobacter GP16 Type IV pilus

+
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