[English] 日本語
Yorodumi
- EMDB-1326: Minute virus of mice, a parvovirus, in complex with the Fab fragm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1326
TitleMinute virus of mice, a parvovirus, in complex with the Fab fragment of a neutralizing monoclonal antibody.
Map dataMinute
Sample
  • Sample: VLPs of Minute Virus of Mice strain i complexed with Fab fragment of neutralizing monoclonal antibody B7
  • Virus: Minute Virus of Mice virus like particles
  • Protein or peptide: B7 Fab fragment
Biological speciesMus (mice) / Minute Virus of Mice virus like particles
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsKaufmann B / Lopez-Bueno A / Garcia-Mateu M / Chipman PR / Nelson CDS / Parrish CR / Almendral JM / Rossmann MG
CitationJournal: J Virol / Year: 2007
Title: Minute virus of mice, a parvovirus, in complex with the Fab fragment of a neutralizing monoclonal antibody.
Authors: Bärbel Kaufmann / Alberto López-Bueno / Mauricio G Mateu / Paul R Chipman / Christian D S Nelson / Colin R Parrish / José M Almendral / Michael G Rossmann /
Abstract: The structure of virus-like particles of the lymphotropic, immunosuppressive strain of minute virus of mice (MVMi) in complex with the neutralizing Fab fragment of the mouse monoclonal antibody (MAb) ...The structure of virus-like particles of the lymphotropic, immunosuppressive strain of minute virus of mice (MVMi) in complex with the neutralizing Fab fragment of the mouse monoclonal antibody (MAb) B7 was determined by cryo-electron microscopy to 7-A resolution. The Fab molecule recognizes a conformational epitope at the vertex of a three-fold protrusion on the viral surface, thereby simultaneously engaging three symmetry-related viral proteins in binding. The location of the epitope close to the three-fold axis is consistent with the previous analysis of MVMi mutants able to escape from the B7 antibody. The binding site close to the symmetry axes sterically forbids the binding of more than one Fab molecule per spike. MAb as well as the Fab molecules inhibits the binding of the minute virus of mice (MVM) to permissive cells but can also neutralize MVM postattachment. This finding suggests that the interaction of B7 with three symmetry-related viral subunits at each spike hinders structural transitions in the viral capsid essential during viral entry.
History
DepositionFeb 15, 2007-
Header (metadata) releaseFeb 23, 2007-
Map releaseNov 15, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.36049481
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.36049481
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1326.gif

Downloads & links

-
Map

FileDownload / File: emd_1326.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMinute
Voxel sizeX=Y=Z: 1.47371 Å
Density
Contour Level1: 4.56 / Movie #1: 4.3604948
Minimum - Maximum-11.138999999999999 - 16.361000000000001
Average (Standard dev.)-1.00496 (±2.4793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-140-140-140
Dimensions280280280
Spacing280280280
CellA=B=C: 412.64 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.47371428571431.47371428571431.4737142857143
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z412.640412.640412.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S312
start NC/NR/NS-140-140-140
NC/NR/NS280280280
D min/max/mean-11.13916.361-1.005

-
Supplemental data

-
Sample components

-
Entire : VLPs of Minute Virus of Mice strain i complexed with Fab fragment...

EntireName: VLPs of Minute Virus of Mice strain i complexed with Fab fragment of neutralizing monoclonal antibody B7
Components
  • Sample: VLPs of Minute Virus of Mice strain i complexed with Fab fragment of neutralizing monoclonal antibody B7
  • Virus: Minute Virus of Mice virus like particles
  • Protein or peptide: B7 Fab fragment

-
Supramolecule #1000: VLPs of Minute Virus of Mice strain i complexed with Fab fragment...

SupramoleculeName: VLPs of Minute Virus of Mice strain i complexed with Fab fragment of neutralizing monoclonal antibody B7
type: sample / ID: 1000
Oligomeric state: twenty Fab fragments bind to one icosahedral virus particle
Number unique components: 2
Molecular weightTheoretical: 4.84 MDa

-
Supramolecule #1: Minute Virus of Mice virus like particles

SupramoleculeName: Minute Virus of Mice virus like particles / type: virus / ID: 1 / Name.synonym: MVMi / Details: icosahedral particle / Sci species name: Minute Virus of Mice virus like particles / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: MVMi
Host (natural)synonym: VERTEBRATES
Molecular weightExperimental: 3.8 MDa
Virus shellShell ID: 1 / Name: VP2 protein shell / Diameter: 280 Å / T number (triangulation number): 1

-
Macromolecule #1: B7 Fab fragment

MacromoleculeName: B7 Fab fragment / type: protein_or_peptide / ID: 1 / Name.synonym: Fab B7 / Details: monomer / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Mus (mice) / synonym: mouse / Cell: hybridoma cell line
Molecular weightExperimental: 50 KDa
Recombinant expressionOrganism: hybridoma cell line (unknown)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 10mM Tris-HCl, 100mM NaCl
GridDetails: 400 mesh copper
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: guillotine-style plunge freezing device
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.198 µm / Nominal defocus min: 2.052 µm / Nominal magnification: 45000
Sample stageSpecimen holder: EUCENTRIC / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: live FFT at 200K
Detailslow dose
DateOct 28, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 14 / Average electron dose: 22 e/Å2 / Od range: 1.15 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

-
Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMPFT, POR, P3DR
Details: final map includes data to 6.8 Ang resolution (fsc 0.3 cut-off); magnification of final map standardized to a map calculated from MVMi model coordinates (PDB accession no 1Z1C) resulting in ...Details: final map includes data to 6.8 Ang resolution (fsc 0.3 cut-off); magnification of final map standardized to a map calculated from MVMi model coordinates (PDB accession no 1Z1C) resulting in final pixel separation of 1.474Ang
Number images used: 6375

-
Atomic model buiding 1

SoftwareName: EMFIT SR5
DetailsProtocol: rigid body. The atomic coordinates of a Fab B7 homology model were fitted into difference map calculated between the MVM-Fab complex and MVM on its own.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Target criteria: sum of density at each atomic positon, lack of atoms in negative density, distance restraints

+
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