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- EMDB-8573: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w... -

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Basic information

Entry
Database: EMDB / ID: 8573
TitleHIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
SampleHIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
SourceHomo sapiens / human
Map dataNegative Stain EM Reconstruction of the DH576 Fab in complex with the HIV CH505 SOSIP.664 trimer
Methodsingle particle reconstruction, at 28.1 Å resolution
AuthorsFera D / Harrison SC
CitationPLoS Pathog., 2017, 13, e1006182-e1006182

PLoS Pathog., 2017, 13, e1006182-e1006182 StrPapers
Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial.
David Easterhoff / M Anthony Moody / Daniela Fera / Hao Cheng / Margaret Ackerman / Kevin Wiehe / Kevin O Saunders / Justin Pollara / Nathan Vandergrift / Rob Parks / Jerome Kim / Nelson L Michael / Robert J O'Connell / Jean-Louis Excler / Merlin L Robb / Sandhya Vasan / Supachai Rerks-Ngarm / Jaranit Kaewkungwal / Punnee Pitisuttithum / Sorachai Nitayaphan / Faruk Sinangil / James Tartaglia / Sanjay Phogat / Thomas B Kepler / S Munir Alam / Hua-Xin Liao / Guido Ferrari / Michael S Seaman / David C Montefiori / Georgia D Tomaras / Stephen C Harrison / Barton F Haynes

DateDeposition: Jan 23, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: Mar 8, 2017 / Last update: Jan 23, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.13
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.13
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8573.map.gz (map file in CCP4 format, 18967 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
2.13 Å/pix.
= 357.84 Å
168 pix
2.13 Å/pix.
= 357.84 Å
168 pix
2.13 Å/pix.
= 357.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.13 Å
Density
Contour Level:2.13 (by author), 2.13 (movie #1):
Minimum - Maximum-17.58503 - 15.786919
Average (Standard dev.)-0.024374684 (1.0161787)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin-84-84-84
Limit838383
Spacing168168168
CellA=B=C: 357.84003 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.132.132.13
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z357.840357.840357.840
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-17.58515.787-0.024

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Supplemental data

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Sample components

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Entire HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w...

EntireName: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
Number of components: 6
MassTheoretical: 50 kDa

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Component #1: protein, HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in ...

ProteinName: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
Recombinant expression: No
MassTheoretical: 50 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK 293T

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Component #2: protein, CH505 Transmitted Founder Envelope

ProteinName: CH505 Transmitted Founder Envelope / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK 293T

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Component #3: protein, DH576 Fab

ProteinName: DH576 Fab / Details: fab fragment / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK 293T

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Component #4: protein, HIV Envelope

ProteinName: HIV Envelope / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / human

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Component #5: protein, DH576 Fab Light Chain

ProteinName: DH576 Fab Light Chain / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / human

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Component #6: protein, DH576 Fab Heavy Chain

ProteinName: DH576 Fab Heavy Chain / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 7.5
Staining2% uranyl formate used to stain sample for 20 s
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
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: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 22929
3D reconstructionSoftware: EMAN2 / Resolution: 28.1 Å / Resolution method: FSC 0.5 CUT-OFF

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