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- EMDB-5268: Three-dimensional structure of Dengue virus serotype 1 complexed ... -

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Basic information

Entry
Database: EMDB / ID: 5268
TitleThree-dimensional structure of Dengue virus serotype 1 complexed with HMAb 14c10 Fab
Keywordsvirus / dengue / serotype 1 / mature virus / human antibody / neutralizing / serotype specific / Fab
SampleDengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10
SourceDengue virus 1 / virus / Dengue 1
Homo sapiens / human
Map datacryo-EM reconstruction of a complex of Dengue serotype 1 with 14C10 antibodies
Methodsingle particle (icosahedral) reconstruction, at 7 A resolution
AuthorsTeoh EP / Kukkaro P / Teo EW / Lim A / Tan TT / Shi PY / Yip A / Schul W / Leo S / Chan SH / Smith KGC / Ooi EE / Kemeny DM / Ng G / Ng ML / Alonso S / Fisher D / Hanson B / Lok SM / MacAry PA
CitationSci Transl Med, 2012, 4, 139ra83-139ra83

Sci Transl Med, 2012, 4, 139ra83-139ra83 StrPapers
The structural basis for serotype-specific neutralization of dengue virus by a human antibody.
Ee Ping Teoh / Petra Kukkaro / En Wei Teo / Angeline P C Lim / Tze Tong Tan / Andy Yip / Wouter Schul / Myint Aung / Victor A Kostyuchenko / Yee Sin Leo / Soh Ha Chan / Kenneth G C Smith / Annie Hoi Yi Chan / Gang Zou / Eng Eong Ooi / D Michael Kemeny / Grace K Tan / Jowin K W Ng / Mah Lee Ng / Sylvie Alonso / Dale Fisher / Pei-Yong Shi / Brendon J Hanson / Shee-Mei Lok / Paul A MacAry

DateDeposition: Mar 15, 2011 / Header (metadata) release: Mar 23, 2011 / Map release: Jun 27, 2012 / Last update: Mar 15, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3j05
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4cau
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_5268.map.gz (map file in CCP4 format, 488283 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
500 pix
1.9 A/pix
= 950. A
500 pix
1.9 A/pix
= 950. A
500 pix
1.9 A/pix
= 950. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.9 A
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-12.80239964 - 18.50806618
Average (Standard dev.)0E-8 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions500500500
Origin-250-250-250
Limit249249249
Spacing500500500
CellA=B=C: 950 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.91.91.9
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z950.000950.000950.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS500500500
D min/max/mean-12.80218.508-0.000

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Supplemental data

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Sample components

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Entire Dengue virus serotype 1 with Fab fragment of human monoclonal ant...

EntireName: Dengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10
Number of components: 2
Oligomeric State: 120 Fab molecules bind to one dengue virion

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Component #1: virus, Dengue virus 1

VirusName: Dengue virus 1 / a.k.a: Dengue 1 / Class: VIRION / Details: strain PVP 159 / Enveloped: Yes / Empty: No / Isolate: STRAIN
SpeciesSpecies: Dengue virus 1 / virus / Dengue 1
Source (natural)Host Species: Aedes albopictus / arthropod / image: Aedes aegypti
Host category: INVERTEBRATES

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Component #2: protein, antibody Fab fragment

ProteinName: antibody Fab fragment / a.k.a: Fab / Oligomeric Details: monomer / Recombinant expression: Yes
MassExperimental: 50 MDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Vector: pTT5
Source (natural)Location in cell: secreted / Cell: CD22plus B cells / Organ or tissue: blood

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 120 mM NaCl, 12 mM Tris-HCl, pH 8.0, 1mM EDTA
pH: 8
Support filmlacey carbon copper grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: 1 second blotting / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS / Date: Sep 27, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 16 e/A2 / Illumination mode: SPOT SCAN
LensMagnification: 47000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 760 - 4900 nm
Specimen HolderModel: OTHER / Temperature: 100 K
CameraDetector: GENERIC GATAN

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Image acquisition

Image acquisitionNumber of digital images: 341 / Sampling size: 15 microns / Bit depth: 16 / Details: 4k x 4k Gatan CCD

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Details: The particles were selected manually. / Number of projections: 2129 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Cross-common lines / Software: EMAN, MPSA / CTF correction: Each particle / Resolution: 7 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: correlation / Refinement space: REAL
Details: Protocol: rigid body. The domains were fitted separately using Fit In Map feature in Chimera
Input PDB model: 3G7T
Output model

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