[English] 日本語
Yorodumi
- EMDB-0069: High-resolution Cryo-EM of Fab-labeled human parechovirus 3 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0069
TitleHigh-resolution Cryo-EM of Fab-labeled human parechovirus 3
Map dataHuman parechovirus type 3 in complex with neutralizing human monoclonal antibody Fabs Post-processed map, B factor -70
SampleHuman parechovirus type 3 in complex with fabs from AT12-015:
virus / fabs from AT12-015 / nucleic-acidNucleic acid / VP0 / VP1 / VP3 / (AT12-015 antibody variable ...) x 2
Function / homologyRNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus capsid / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Viral polyprotein, parechovirus P3B / Viral polyprotein, parechovirus P3A / P-loop containing nucleoside triphosphate hydrolase / Picornaviridae P3A protein ...RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus capsid / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Viral polyprotein, parechovirus P3B / Viral polyprotein, parechovirus P3A / P-loop containing nucleoside triphosphate hydrolase / Picornaviridae P3A protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / picornavirus capsid protein / 3C cysteine protease (picornain 3C) / RNA dependent RNA polymerase / RNA helicase / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Parechovirus Genome-linked protein / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / viral genome / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / viral capsid / ion channel activity / protein complex oligomerization / viral RNA genome replication / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / virion attachment to host cell / transcription, DNA-templated / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
SourceHuman parechovirus 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 2.8 Å resolution
AuthorsDomanska A / Flatt JW / Jukonen JJJ / Geraets JA / Butcher SJ
CitationJournal: J. Virol. / Year: 2018
Title: 2.8 Å resolution cryo-EM structure of human parechovirus 3 in complex with Fab from a neutralizing antibody.
Authors: Aušra Domanska / Justin W Flatt / Joonas J J Jukonen / James A Geraets / Sarah J Butcher
Abstract: Human parechovirus 3 (HPeV3) infection is associated with sepsis in neonates characterized by significant immune activation and subsequent tissue damage. Strategies to limit infection have been ...Human parechovirus 3 (HPeV3) infection is associated with sepsis in neonates characterized by significant immune activation and subsequent tissue damage. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and lack of a vaccine or specific antiviral therapy. Towards the latter, we present a 2.8 Å-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody AT12-015 using cryo-EM and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally at high-resolution, it was possible to model a stretch of RNA inside the virion and from this identify the key features that drive and stabilize protein-RNA association during assembly. HPeV3 is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, which despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Towards this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high-resolution it was possible to precisely define the epitope that when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interaction, viral pathogenesis mechanisms, and for finding potential cures for infection and disease.
Validation ReportPDB-ID: 6gv4

SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2018 / Header (metadata) release: Jul 18, 2018 / Map release: Nov 21, 2018 / Last update: Dec 5, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6gv4
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0069.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.06 Å/pix.
= 508.8 Å
480 pix
1.06 Å/pix.
= 508.8 Å
480 pix
1.06 Å/pix.
= 508.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.19998817 - 0.41895282
Average (Standard dev.)0.0015927622 (0.024973061)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin0.00.0-479.0
Limit479.0479.00.0
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-240-240-240
NC/NR/NS480480480
D min/max/mean-0.2000.4190.002

-
Supplemental data

-
Sample components

+
Entire Human parechovirus type 3 in complex with fabs from AT12-015

EntireName: Human parechovirus type 3 in complex with fabs from AT12-015
Number of components: 9

+
Component #1: protein, Human parechovirus type 3 in complex with fabs from AT12-015

ProteinName: Human parechovirus type 3 in complex with fabs from AT12-015
Recombinant expression: No
MassTheoretical: 7.7 MDa

+
Component #2: virus, Human parechovirus 3

VirusName: Human parechovirus 3 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human parechovirus 3 / Strain: A308/99

+
Component #3: protein, fabs from AT12-015

ProteinName: fabs from AT12-015 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: nucleic-acid, RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3')

Nucleic-acidName: RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3') / Class: RNA / Details: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGGUAUUU
MassTheoretical: 2.505489 kDa
SourceSpecies: Human parechovirus 3

+
Component #5: protein, VP0

ProteinName: VP0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.770135 kDa
SourceSpecies: Human parechovirus 3
Source (natural)Organ or tissue: colon adenocarcinoma

+
Component #6: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.913127 kDa
SourceSpecies: Human parechovirus 3
Source (natural)Organ or tissue: colon adenocarcinoma

+
Component #7: protein, VP3

ProteinName: VP3 / Details: polypeptide chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.757551 kDa
SourceSpecies: Human parechovirus 3
Source (natural)Organ or tissue: colon adenocarcinoma

+
Component #8: protein, AT12-015 antibody variable heavy

ProteinName: AT12-015 antibody variable heavy / Details: polypeptide chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128613 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #9: protein, AT12-015 antibody variable light

ProteinName: AT12-015 antibody variable light / Details: polypeptide chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.339752 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.5
Support filmultrathin carbon-coated lacey 400-mesh copper grids (Ted Pella product #01824)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 295 K
Details: We could not control humidity during plunging. It was ambient humidity. Blot for 1 s before plunging..

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 6541

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 74927
3D reconstructionSoftware: RELION / CTF correction: GCTF was used to estimate ctf / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement space: REAL
Details: Initial model was generated in I-TASSER and SWISSMODEL using 4z92 and 4udf as reference. Initial rigid fit of the model to the map was done in UCSF Chimera. Model refinement was done in Coot and MDFF.
Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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