[English] 日本語
Yorodumi
- EMDB-1418: Binding of a neutralizing antibody to dengue virus alters the arr... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1418
TitleBinding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins
SampleFab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
SourceDengue virus 2 / virus / DENV
Mus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /
Map dataThis is a map of Fab 1A1D-2 complexed with Dengue virus
Methodsingle particle (icosahedral) reconstruction, at 24 A resolution
AuthorsLok SM
CitationNat. Struct. Mol. Biol., 2008, 15, 312-317

Nat. Struct. Mol. Biol., 2008, 15, 312-317 StrPapers
Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins.
Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / Michael S Diamond / Richard J Kuhn / Michael G Rossmann

DateDeposition: Sep 7, 2007 / Header (metadata) release: Sep 7, 2007 / Map release: Jan 2, 2008 / Last update: Sep 7, 2007

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.98
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1.98
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-2r6p
  • Surface level: 1.98
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_1418.map.gz (map file in CCP4 format, 93313 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
2.74 A/pix
= 789.12 A
288 pix
2.74 A/pix
= 789.12 A
288 pix
2.74 A/pix
= 789.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.74 A
Density
Contour Level:1.98, 1.98 (movie #1):
Minimum - Maximum-4.12769 - 8.46468
Average (Standard dev.)0.00957931 (0.995975)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin-144-144-144
Limit143143143
Spacing288288288
CellA=B=C: 789.12 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.742.742.74
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z789.120789.120789.120
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-30-30-49
NX/NY/NZ6060100
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
D min/max/mean-4.1288.4650.010

-
Supplemental data

-
Sample components

-
Entire Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus

EntireName: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
Oligomeric State: The Fab molecule binds to two of the three E proteins in the icosahedral assymmetric unit
Number of components: 2

-
Component #1: virus, Dengue virus 2

VirusName: Dengue virus 2 / a.k.a: DENV / Class: VIRION / Enveloped: Yes / Empty: No / Isolate: SEROTYPE
SpeciesSpecies: Dengue virus 2 / virus / DENV
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
Shell #1Name of element: envelope / Diameter: 240 A / T number(triangulation number): 3

-
Component #2: protein, Fab fragment of MAb 1A1D-2

ProteinName: Fab fragment of MAb 1A1D-2 / a.k.a: 1A1D-2 / Oligomeric Details: heterodimer / Recombinant expression: No / Number of Copies: 2
MassTheoretical: 50 MDa / Experimental: 50 MDa
SourceSpecies: Mus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /
Source (natural)Cell: hybridoma

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.6 mg/ml / Buffer solution: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA / pH: 7.6
Support film400 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
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.
Details: Vitrification instrument: Guillotine-style plunge freezeing device

-
Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200T / Date: Mar 21, 2007 / Details: low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 51040 X (calibrated) / Astigmatism: live FFT / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2270 - 3370 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionSampling size: 7 microns

-
Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 2885 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: projection matching / Software: spider,XMIPP / CTF correction: each particle / Resolution: 24 A / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Software: EMFIT / Refinement protocol: rigid body / Details: Protocol: Rigid body
Input PDB model: 1THD
Chain ID: 2R29
Output model

+
About Yorodumi

-
News

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more