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- EMDB-8507: 92BR SOSIP.664 trimer in complex with DH270.1 Fab -

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Basic information

Entry
Database: EMDB / ID: 8507
Title92BR SOSIP.664 trimer in complex with DH270.1 Fab
Sample92BR HIV Env SOSIP and DH720.1 Fab
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataDH270.1 Fab in complex with 92BR SOSIP.664
Methodsingle particle reconstruction, at 29.4 A resolution
AuthorsFera D / Harrison SC
CitationSci Transl Med, 2017, 9

Sci Transl Med, 2017, 9 StrPapers
Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O Saunders / Ruijun Zhang / Morgan A Gladden / Anthony Monroe / Amit Kumar / Shi-Mao Xia / Melissa Cooper / Mark K Louder / Krisha McKee / Robert T Bailer / Brendan W Pier / Claudia A Jette / Garnett Kelsoe / Wilton B Williams / Lynn Morris / John Kappes / Kshitij Wagh / Gift Kamanga / Myron S Cohen / Peter T Hraber / David C Montefiori / Ashley Trama / Hua-Xin Liao / Thomas B Kepler / M Anthony Moody / Feng Gao / Samuel J Danishefsky / John R Mascola / George M Shaw / Beatrice H Hahn / Stephen C Harrison / Bette T Korber / Barton F Haynes

DateDeposition: Dec 5, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Mar 15, 2017 / Last update: Dec 5, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.28
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.28
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8507.map.gz (map file in CCP4 format, 18967 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.13 A
Density
Contour Level:3.28 (by author), 3.28 (movie #1):
Minimum - Maximum-31.809095 - 25.922125
Average (Standard dev.)-0.055014014 (1.659475)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin-84-84-84
Limit838383
Spacing168168168
CellA=B=C: 357.84003 A
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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-31.80925.922-0.055

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Supplemental data

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Sample components

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Entire 92BR HIV Env SOSIP and DH720.1 Fab

EntireName: 92BR HIV Env SOSIP and DH720.1 Fab / Number of components: 1

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Component #1: protein, 92BR HIV Env SOSIP and DH720.1 Fab

ProteinName: 92BR HIV Env SOSIP and DH720.1 Fab / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Homo sapiens / human / Vector: pVRC-8400 / Cell of expression system: HEK293T

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Experimental details

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Sample preparation

Specimen state2D array
Sample solutionSpecimen conc.: 0.01 mg/ml
Buffer solution: 10 mM HEPES, pH 8.0, 150 mM NaCl, 0.02% sodium azide
pH: 8
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 5419
3D reconstructionSoftware: EMAN / Resolution: 29.4 A / Resolution method: FSC 0.5 CUT-OFF

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