[English] 日本語
Yorodumi
- EMDB-8285: expanded poliovirus in complex with VHH 17B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8285
Titleexpanded poliovirus in complex with VHH 17B
Map dataexpanded poliovirus in complex with VHH 17B
Sample
  • Complex: expanded poliovirus in complex with VHH 17B
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VHH 17B
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPoliovirus type 1 (strain Mahoney) / Camelus dromedarius (Arabian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsStrauss M / Schotte L / Filman DJ / Hogle JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI020566 United States
CitationJournal: J Virol / Year: 2017
Title: Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.
Authors: Mike Strauss / Lise Schotte / Krishanthi S Karunatilaka / David J Filman / James M Hogle /
Abstract: By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs ...By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion.
IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The ...IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events.
History
DepositionJul 23, 2016-
Header (metadata) releaseSep 28, 2016-
Map releaseNov 2, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00599
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00599
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5ku0
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ku0
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8285.png

Downloads & links

-
Map

FileDownload / File: emd_8285.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationexpanded poliovirus in complex with VHH 17B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 422.144 Å		0.82 Å/pix.
x 512 pix.
= 422.144 Å		0.82 Å/pix.
x 512 pix.
= 422.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00599 / Movie #1: 0.00599
Minimum - Maximum-0.0054358235 - 0.019437835
Average (Standard dev.)-0.000620336 (±0.003170661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 422.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.82450.82450.8245
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z422.144422.144422.144
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.0050.019-0.001

-
Supplemental data

-
Sample components

-
Entire : expanded poliovirus in complex with VHH 17B

EntireName: expanded poliovirus in complex with VHH 17B
Components
  • Complex: expanded poliovirus in complex with VHH 17B
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VHH 17B

-
Supramolecule #1: expanded poliovirus in complex with VHH 17B

SupramoleculeName: expanded poliovirus in complex with VHH 17B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Poliovirus type 1 (strain Mahoney)
Molecular weightTheoretical: 9 MDa

-
Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Molecular weightTheoretical: 25.291594 KDa
SequenceString: PSDTVQTRHV VQHRSRSESS IESFFARGAC VTIMTVDNPA STTNKDKLFA VWKITYKDTV QLRRKLEFFT YSRFDMELTF VVTANFTET NNGHALNQVY QIMYVPPGAP VPEKWDDYTW QTSSNPSIFY TYGTAPARIS VPYVGISNAY SHFYDGFSKV P LKDQSAAL ...String:
PSDTVQTRHV VQHRSRSESS IESFFARGAC VTIMTVDNPA STTNKDKLFA VWKITYKDTV QLRRKLEFFT YSRFDMELTF VVTANFTET NNGHALNQVY QIMYVPPGAP VPEKWDDYTW QTSSNPSIFY TYGTAPARIS VPYVGISNAY SHFYDGFSKV P LKDQSAAL GDSIYGAASL NDFGILAVRV VNDHNPTKVT SKIRVYLKPK HIRVWCPRPP RAVAY

-
Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Molecular weightTheoretical: 29.677301 KDa
SequenceString: SPNIEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPDVAA CRFYTLDTVS WTKESRGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG T FTPDNNQT ...String:
SPNIEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPDVAA CRFYTLDTVS WTKESRGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG T FTPDNNQT SPARRFCPVD YLLGNGTLLG NAFVFPHQII NLRTNNCATL VLPYVNSLSI DSMVKHNNWG IAILPLAPLN FA SESSPEI PITLTIAPMC CEFNGLRNIT LP

-
Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Molecular weightTheoretical: 25.777613 KDa
SequenceString: GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRQ TIDDSFTEGG YISVFYQTRI VVPLSTPREM DILGFVSACN DFSVRLLRDT THI

-
Macromolecule #4: VHH 17B

MacromoleculeName: VHH 17B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus dromedarius (Arabian camel)
Molecular weightTheoretical: 13.262598 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLQESGGG LVQPGGSLTL SCAASGYAVS RYSMGWFRQA PGKENEGVAA IDSSGVGTTY ADSVKGRFTI SRDNAKDTVY LRMNSLKPE DTAIYYCASG FGLSLSRYTY AYWGQGTQVT VSSHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1hxs


Details: a map was generated from the PDB and lowpass filtered to 6nm
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: GeFrealign, FREALIGN (ver. 9.09)) / Number images used: 17654
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9)

-
Atomic model buiding 1

Detailsusing both Fourier amplitudes and phases
RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5ku0:
expanded poliovirus in complex with VHH 17B

+
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