[English] 日本語
Yorodumi
- EMDB-6148: Cryo-EM reconstruction of poliovirus-receptor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6148
TitleCryo-EM reconstruction of poliovirus-receptor complex
Map dataReconstruction of receptor-decorated poliovirus at 0.4 nm resolution, sharpened with a B-factor of -60
Sample
  • Sample: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
  • Virus: Human poliovirus 1 Mahoney
  • Protein or peptide: Poliovirus receptor
Keywordspoliovirus / receptor / PVR / CD155
Function / homology
Function and homology information


susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / virus receptor activity / focal adhesion / cell surface / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Human poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsStrauss M / Filman DJ / Cheng N / Noel RT / Belnap DM / Hogle JM
CitationJournal: J Virol / Year: 2015
Title: Nectin-like interactions between poliovirus and its receptor trigger conformational changes associated with cell entry.
Authors: Mike Strauss / David J Filman / David M Belnap / Naiqian Cheng / Roane T Noel / James M Hogle /
Abstract: Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to ...Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to form an expanded form of the capsid called the 135S particle. This expansion results in the externalization of the myristoylated capsid protein VP4 and the N-terminal extension of the capsid protein VP1, both of which become inserted into the cell membrane. Structures of the expanded forms of poliovirus and of several related viruses have recently been reported. However, until now, it has been unclear how receptor binding triggers viral expansion at physiological temperature. Here, we report poliovirus in complex with an enzymatically partially deglycosylated form of the 3-domain ectodomain of Pvr at a 4-Å resolution, as determined by cryo-electron microscopy. The interaction of the receptor with the virus in this structure is reminiscent of the interactions of Pvr with its natural ligands. At a low temperature, the receptor induces very few changes in the structure of the virus, with the largest changes occurring within the footprint of the receptor, and in a loop of the internal protein VP4. Changes in the vicinity of the receptor include the displacement of a natural lipid ligand (called "pocket factor"), demonstrating that the loss of this ligand, alone, is not sufficient to induce particle expansion. Finally, analogies with naturally occurring ligand binding in the nectin family suggest which specific structural rearrangements in the virus-receptor complex could help to trigger the irreversible expansion of the capsid.
IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into ...IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into three-dimensional experimental maps of the receptor-virus complex. The molecular interactions we see between poliovirus and its receptor are reminiscent of the nectin family, by involving the burying of otherwise-exposed hydrophobic groups. Importantly, poliovirus expansion is regulated by the binding of a lipid molecule within the viral capsid. We show that receptor binding either causes this molecule to be expelled or requires it, but that its loss is not sufficient to trigger irreversible expansion. Based on our model, we propose testable hypotheses to explain how the viral shell becomes destabilized, leading to RNA uncoating. These findings give us a better understanding of how poliovirus has evolved to exploit a natural process of its host to penetrate the membrane barrier.
History
DepositionOct 15, 2014-
Header (metadata) releaseNov 26, 2014-
Map releaseFeb 4, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6148.gif

Downloads & links

-
Map

FileDownload / File: emd_6148.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of receptor-decorated poliovirus at 0.4 nm resolution, sharpened with a B-factor of -60
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 640 pix.
= 631.04 Å		0.99 Å/pix.
x 640 pix.
= 631.04 Å		0.99 Å/pix.
x 640 pix.
= 631.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.986 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.03553775 - 0.06540409
Average (Standard dev.)-0.00157756 (±0.00659506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-319-319-319
Dimensions640640640
Spacing640640640
CellA=B=C: 631.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9860.9860.986
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z631.040631.040631.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-319-319-319
NC/NR/NS640640640
D min/max/mean-0.0360.065-0.002

-
Supplemental data

-
Sample components

-
Entire : Type I poliovirus (Mahoney) in complex with enzymatically deglyco...

EntireName: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
Components
  • Sample: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
  • Virus: Human poliovirus 1 Mahoney
  • Protein or peptide: Poliovirus receptor

-
Supramolecule #1000: Type I poliovirus (Mahoney) in complex with enzymatically deglyco...

SupramoleculeName: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
type: sample / ID: 1000 / Oligomeric state: 1 icosahedral virus + 60 receptors / Number unique components: 2
Molecular weightTheoretical: 12 MDa

-
Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 9 MDa
Virus shellShell ID: 1 / Diameter: 165 Å / T number (triangulation number): 1

-
Macromolecule #1: Poliovirus receptor

MacromoleculeName: Poliovirus receptor / type: protein_or_peptide / ID: 1 / Name.synonym: PVR/CD155, Nectin-like protein 5, NECL-5 / Number of copies: 60 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Poliovirus receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7 / Details: PBS
GridDetails: 200 mesh Cu grid with fenestrated carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 45 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Method: Sample mixed and frozen within 2 minutes.

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 165 K / Average: 100 K
Alignment procedureLegacy - Electron beam tilt params: 0
DetailsK2 Summit super-resolution mode used
DateNov 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 2.5 µm / Number real images: 280 / Average electron dose: 25 e/Å2 / Details: The last 22 frames of a 24-frame stack were used. / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 25355 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 27500
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: per micrograph
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: Relion1.2, GeFrealign / Details: This map has a B-factor of -60 applied to it. / Number images used: 9248

-
Atomic model buiding 1

Initial modelPDB ID:

1hxs


Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 2 / Chain - #2 - Chain ID: 3 / Chain - #3 - Chain ID: 4
SoftwareName: Coot, spdbv, Refmac5
DetailsAfter rigid-body fitting, manual model building was alternated with automated stereochemically restrained refinement, minimizing the discrepancy between experimental and model-based Fourier amplitudes and phases.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: pseudo-real space

-
Atomic model buiding 2

Initial modelPDB ID:

4fqp


Chain - Chain ID: A
SoftwareName: Coot, spdbv, Refmac5
DetailsAfter rigid-body fitting, manual model building was alternated with automated stereochemically restrained refinement, minimizing the discrepancy between experimental and model-based Fourier amplitudes and phases.
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: pseudo-real space

+
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