[English] 日本語
Yorodumi
- PDB-3j3z: Structure of MA28-7 neutralizing antibody Fab fragment from elect... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j3z
TitleStructure of MA28-7 neutralizing antibody Fab fragment from electron cryo-microscopy of enterovirus 71 complexed with a Fab fragment
Components
  • MA28-7 neutralizing antibody heavy chain
  • MA28-7 neutralizing antibody light chain
KeywordsIMMUNE SYSTEM / EV71 / enterovirus / HFMD / strain-specific eptitope / VP1-145
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 23.4 Å
AuthorsLee, H. / Cifuente, J.O. / Ashley, R.E. / Conway, J.F. / Makhov, A.M. / Tano, Y. / Shimizu, H. / Nishimura, Y. / Hafenstein, S.
CitationJournal: J Virol / Year: 2013
Title: A strain-specific epitope of enterovirus 71 identified by cryo-electron microscopy of the complex with fab from neutralizing antibody.
Authors: Hyunwook Lee / Javier O Cifuente / Robert E Ashley / James F Conway / Alexander M Makhov / Yoshio Tano / Hiroyuki Shimizu / Yorihiro Nishimura / Susan Hafenstein /
Abstract: Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 ...Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 induces severe neuropathology leading to high fatalities, especially among children under the age of 6 years. Currently, no established vaccines or treatments are available against EV71 infection. The monoclonal antibody MA28-7 neutralizes only specific strains of EV71 that have a conserved glycine at amino acid VP1-145, a surface-exposed residue that maps to the 5-fold vertex and that has been implicated in receptor binding. The cryo-electron microscopy structure of a complex between EV71 and the Fab fragment of MA28-7 shows that only one Fab fragment occupies each 5-fold vertex. A positively charged patch, which has also been implicated in receptor binding, lies within the Fab footprint. We identify the strain-specific epitope of EV71 and discuss the possible neutralization mechanisms of the antibody.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5673
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5673
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: MA28-7 neutralizing antibody light chain
H: MA28-7 neutralizing antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)46,6112
Polymers46,6112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Antibody MA28-7 neutralizing antibody light chain


Mass: 23261.770 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody MA28-7 neutralizing antibody heavy chain


Mass: 23349.105 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody
Type: VIRUS
Molecular weightValue: 8.05 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.5 / Details: 10 mM Tris, 200 mM NaCl, 50 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon Quantifoil electron microscopy grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temp: 76 K / Humidity: 95 %
Details: Plunged into ethane-propane mixture (FEI VITROBOT MARK III)

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 2, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 48425 X / Nominal defocus max: 6120 nm / Nominal defocus min: 1900 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 45
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EMAN23D reconstruction
CTF correctionDetails: Each
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Cross correlation coefficient / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 27026 / Nominal pixel size: 1.23 Å / Actual pixel size: 1.23 Å
Details: The breaksym option in EMAN2 was used to search for the icosahedrally-related orientations. (Single particle details: Selected particles were low-pass filtered at 10 Angstrom. Asymmetric ...Details: The breaksym option in EMAN2 was used to search for the icosahedrally-related orientations. (Single particle details: Selected particles were low-pass filtered at 10 Angstrom. Asymmetric reconstruction was performed with the breaksym option in EMAN2.) (Single particle--Applied symmetry: C1)
Num. of class averages: 2300 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Details: REFINEMENT PROTOCOL--rigid body DETAILS--The Fab structure was fitted manually, then refined in Chimera.
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
13GK8

3gk8

H1
23GK8

3gk8

L1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 0 3283

+
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