[English] 日本語
Yorodumi
- EMDB-5765: A new topology of the HK97-like fold revealed in Bordetella bacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5765
TitleA new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5A resolution
Map dataAveraged MCP density of Bordetella bacteriophage (EMD-5764)
Sample
  • Sample: Bordetella bacteriophage major capsid protein (MCP)
  • Protein or peptide: major capsid protein
KeywordsProtein topology / HK97 like / cryoEM / bacteriophage
Biological speciesBordetella phage BPP-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang X / Guo H / Jin L / Czornyj E / Hodes A / Hui WH / Nieh AW / Miller JF / Zhou ZH
CitationJournal: Elife / Year: 2013
Title: A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution.
Authors: Xing Zhang / Huatao Guo / Lei Jin / Elizabeth Czornyj / Asher Hodes / Wong H Hui / Angela W Nieh / Jeff F Miller / Z Hong Zhou /
Abstract: Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering ...Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like ('Johnson') for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001.
History
DepositionOct 10, 2013-
Header (metadata) releaseOct 23, 2013-
Map releaseDec 25, 2013-
UpdateJan 8, 2014-
Current statusJan 8, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j4u
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j4u
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5765.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged MCP density of Bordetella bacteriophage (EMD-5764)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-4.30249977 - 8.001859659999999
Average (Standard dev.)0.0045297 (±0.13196595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-95-75153
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S213
start NC/NR/NS-75-95153
NC/NR/NS200200200
D min/max/mean-4.3028.0020.005

-
Supplemental data

-
Sample components

-
Entire : Bordetella bacteriophage major capsid protein (MCP)

EntireName: Bordetella bacteriophage major capsid protein (MCP)
Components
  • Sample: Bordetella bacteriophage major capsid protein (MCP)
  • Protein or peptide: major capsid protein

-
Supramolecule #1000: Bordetella bacteriophage major capsid protein (MCP)

SupramoleculeName: Bordetella bacteriophage major capsid protein (MCP) / type: sample / ID: 1000 / Details: This is the averaged MCP density of EMD-5764. / Number unique components: 1

-
Macromolecule #1: major capsid protein

MacromoleculeName: major capsid protein / type: protein_or_peptide / ID: 1 / Name.synonym: MCP / Details: This is the averaged MCP density of EMD-5764. / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bordetella phage BPP-1 (virus) / synonym: Bordetella bacteriophage

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 50 mM Tris-HCl, 250 mM NaCl
GridDetails: 400 mesh holey carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 57660 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: manual correction / Legacy - Electron beam tilt params: 0
DateJul 12, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 895 / Average electron dose: 25 e/Å2 / Bits/pixel: 2
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle
Final two d classificationNumber classes: 1
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: eLite3D, Frealign / Details: This is the averaged MCP density of EMD-5764. / Number images used: 39549

+
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