[English] 日本語
Yorodumi
- PDB-8twc: Acinetobacter phage AP205 T=3 VLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8twc
TitleAcinetobacter phage AP205 T=3 VLP
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / Acinetobacter / SsRNA phage virus / VIRUS / VLP
Function / homology: / AP205 coat protein / viral capsid / Coat protein
Function and homology information
Biological speciesAcinetobacter phage AP205 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 20, 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
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AB: Coat protein
AC: Coat protein
AD: Coat protein
AE: Coat protein
AF: Coat protein
AG: Coat protein
AH: Coat protein
AI: Coat protein
AJ: Coat protein
AK: Coat protein
AL: Coat protein
AM: Coat protein
AN: Coat protein
AO: Coat protein
AP: Coat protein
AQ: Coat protein
AR: Coat protein
AS: Coat protein
AT: Coat protein
AU: Coat protein
AV: Coat protein
AW: Coat protein
AX: Coat protein
AY: Coat protein
AZ: Coat protein
BA: Coat protein
BB: Coat protein
BC: Coat protein
BD: Coat protein
BE: Coat protein
BF: Coat protein
BG: Coat protein
BH: Coat protein
BI: Coat protein
BJ: Coat protein
BK: Coat protein
BL: Coat protein
BM: Coat protein
BN: Coat protein
BO: Coat protein
BP: Coat protein
BQ: Coat protein
BR: Coat protein
BS: Coat protein
BT: Coat protein
BU: Coat protein
BV: Coat protein
BW: Coat protein
BX: Coat protein
BY: Coat protein
BZ: Coat protein
CA: Coat protein
CB: Coat protein
CC: Coat protein
CD: Coat protein
CE: Coat protein
CF: Coat protein
CG: Coat protein
CH: Coat protein
CI: Coat protein
CJ: Coat protein
CK: Coat protein
CL: Coat protein
CM: Coat protein
CN: Coat protein
CO: Coat protein
CP: Coat protein
CQ: Coat protein
CR: Coat protein
CS: Coat protein
CT: Coat protein
CU: Coat protein
CV: Coat protein
CW: Coat protein
CX: Coat protein
CY: Coat protein
CZ: Coat protein
DA: Coat protein
DB: Coat protein
DC: Coat protein
DD: Coat protein
DE: Coat protein
DF: Coat protein
DG: Coat protein
DH: Coat protein
DI: Coat protein
DJ: Coat protein
DK: Coat protein
DL: Coat protein
DM: Coat protein
DN: Coat protein
DO: Coat protein
DP: Coat protein
DQ: Coat protein
DR: Coat protein
DS: Coat protein
DT: Coat protein
DU: Coat protein
DV: Coat protein
DW: Coat protein
DX: Coat protein
DY: Coat protein
DZ: Coat protein
EA: Coat protein
EB: Coat protein
EC: Coat protein
ED: Coat protein
EE: Coat protein
EF: Coat protein
EG: Coat protein
EH: Coat protein
EI: Coat protein
EJ: Coat protein
EK: Coat protein
EL: Coat protein
EM: Coat protein
EN: Coat protein
EO: Coat protein
EP: Coat protein
EQ: Coat protein
ER: Coat protein
ES: Coat protein
ET: Coat protein
EU: Coat protein
EV: Coat protein
EW: Coat protein
EX: Coat protein
EY: Coat protein
EZ: Coat protein
FA: Coat protein
FB: Coat protein
FC: Coat protein
FD: Coat protein
FE: Coat protein
FF: Coat protein
FG: Coat protein
FH: Coat protein
FI: Coat protein
FJ: Coat protein
FK: Coat protein
FL: Coat protein
FM: Coat protein
FN: Coat protein
FO: Coat protein
FP: Coat protein
FQ: Coat protein
FR: Coat protein
FS: Coat protein
FT: Coat protein
FU: Coat protein
FV: Coat protein
FW: Coat protein
FX: Coat protein
FY: Coat protein
FZ: Coat protein
GA: Coat protein
GB: Coat protein
GC: Coat protein
GD: Coat protein
GE: Coat protein
GF: Coat protein
GG: Coat protein
GH: Coat protein
GI: Coat protein
GJ: Coat protein
GK: Coat protein
GL: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GP: Coat protein
GQ: Coat protein
GR: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GV: Coat protein
GW: Coat protein
GX: Coat protein
GY: Coat protein


Theoretical massNumber of molelcules
Total (without water)2,487,702180
Polymers2,487,702180
Non-polymers00
Water00
1


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

-
Components

#1: Protein ...
Coat protein


Mass: 13820.569 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ42
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Acinetobacter phage AP205 / Type: VIRUS
Details: amplified and purified from infected Acinetobacter GP16 cells.
Entity ID: all / Source: NATURAL
Molecular weightValue: 2.48 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Acinetobacter genomosp. 16BJ
Virus shellName: Coat / Diameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 8 / Details: 20mM Tris-HCl, 150mM NaCl, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris (hydroxymethyl) aminomethane (THAM) hydrochlorideTris-HCl1
2150 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: AP205 virion particle
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3uL sample applied to a 300-mesh 2/1 copper 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 FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
9PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003177300
ELECTRON MICROSCOPYf_angle_d0.566241560
ELECTRON MICROSCOPYf_dihedral_angle_d4.31424480
ELECTRON MICROSCOPYf_chiral_restr0.04328800
ELECTRON MICROSCOPYf_plane_restr0.00631320

+
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