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- EMDB-8578: Negative Stain EM of C05 mutant Fab (VPGSGW) and CR9114 Fab in co... -

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Basic information

Entry
Database: EMDB / ID: 8578
TitleNegative Stain EM of C05 mutant Fab (VPGSGW) and CR9114 Fab in complex with H1 HA Trimer
SampleNegative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs in complex with H1 HA trimer.
SourceInfluenza A virus (A/Solomon Islands/3/2006(H1N1)) / virus
Map dataEM negative stain map of CR9114 and VPGSGW fabs in complex with H1 hemagglutinin trimer.
Methodsingle particle reconstruction, at 18 Å resolution
AuthorsTurner HL / Ward AB
CitationNat Commun, 2017, 8, 15371-15371

Nat Commun, 2017, 8, 15371-15371 Yorodumi Papers
In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity.
Nicholas C Wu / Geramie Grande / Hannah L Turner / Andrew B Ward / Jia Xie / Richard A Lerner / Ian A Wilson

DateDeposition: Feb 1, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: May 31, 2017 / Last update: May 31, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 20.7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 20.7
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8578.map.gz (map file in CCP4 format, 11944 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.05 Å/pix.
= 295.2 Å
144 pix
2.05 Å/pix.
= 295.2 Å
144 pix
2.05 Å/pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.05 Å
Density
Contour Level:20.7 (by author), 20.7 (movie #1):
Minimum - Maximum-48.753773 - 100.832436
Average (Standard dev.)0.7061781 (8.199496)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin000
Limit143143143
Spacing144144144
CellA=B=C: 295.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z295.200295.200295.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-48.754100.8320.706

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Supplemental data

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Sample components

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Entire Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs ...

EntireName: Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs in complex with H1 HA trimer.
Number of components: 1

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Component #1: protein, Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9...

ProteinName: Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs in complex with H1 HA trimer.
Recombinant expression: No
SourceSpecies: Influenza A virus (A/Solomon Islands/3/2006(H1N1)) / virus
Strain: A/Solomon Islands/3/2006(H1N1)
Source (engineered)Expression System: Drosophila / arthropod / image: Drosophila melanogaster

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.019 mg/ml
Buffer solution: Solution was made fresh using 0.2um filter.
pH: 7.4
Staining0.2% Uranyl Formate. Samples were placed on 400 mesh copper grids covered with nitrocellulose. Samples were blotted off and UF was added for a total of 30 seconds before being blotted off.
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 93

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 18874
3D reconstructionAlgorithm: BACK PROJECTION / Software: sxali3d.py / Resolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF

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