[English] 日本語
Yorodumi
- PDB-8tob: Acinetobacter GP16 Type IV pilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tob
TitleAcinetobacter GP16 Type IV pilus
Components(Fimbrial protein) x 2
KeywordsCELL ADHESION / T4P / Competence
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsMeng, R. / Xing, Z. / Zhang, J.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
GA: Fimbrial protein
HA: Fimbrial protein
IA: Fimbrial protein
JA: Fimbrial protein
KA: Fimbrial protein
LA: Fimbrial protein
MA: Fimbrial protein
NA: Fimbrial protein
OA: Fimbrial protein
PA: Fimbrial protein
QA: Fimbrial protein
RA: Fimbrial protein
SA: Fimbrial protein
TA: Fimbrial protein
UA: Fimbrial protein
VA: Fimbrial protein
AA: Fimbrial protein
BA: Fimbrial protein
CA: Fimbrial protein
DA: Fimbrial protein
EA: Fimbrial protein
FA: Fimbrial protein
GB: Fimbrial protein
HB: Fimbrial protein
IB: Fimbrial protein
JB: Fimbrial protein
KB: Fimbrial protein
LB: Fimbrial protein
MB: Fimbrial protein
NB: Fimbrial protein
OB: Fimbrial protein
PB: Fimbrial protein
QB: Fimbrial protein
RB: Fimbrial protein
SB: Fimbrial protein
TB: Fimbrial protein
UB: Fimbrial protein
VB: Fimbrial protein
AB: Fimbrial protein
BB: Fimbrial protein
CB: Fimbrial protein
DB: Fimbrial protein
EB: Fimbrial protein
FB: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)318,35244
Polymers318,35244
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Fimbrial protein


Mass: 7470.747 Da / Num. of mol.: 22 / Fragment: residues 9-78 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9
#2: Protein ...
Fimbrial protein


Mass: 6999.778 Da / Num. of mol.: 22 / Fragment: residues 79-147 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Acinetobacter genomosp.16 Tyoe IV pilus / Type: COMPLEX / Details: Filamentous Type IV pilus / Entity ID: all / Source: NATURAL
Molecular weightValue: 11 kDa/nm / Experimental value: NO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Buffer solutionpH: 8 / Details: 20mM Tris-HCl, 200mM NaCl, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris (hydroxymethyl) aminomethane (THAM) hydrochlorideTris-HClTris1
2200 mMSodium ChlorideNaClSodium chloride1
SpecimenConc.: 1.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: vitreous Typy IV pilus
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3uL sample applied to a QuantiFoil R2/1 grid

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 135000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 92 ° / Axial rise/subunit: 10 Å / Axial symmetry: C1
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 900000 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222528
ELECTRON MICROSCOPYf_angle_d0.42830712
ELECTRON MICROSCOPYf_dihedral_angle_d3.9923146
ELECTRON MICROSCOPYf_chiral_restr0.0383916
ELECTRON MICROSCOPYf_plane_restr0.0033784

+
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