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- EMDB-8950: Cryo-EM structure at 3.5 A resolution of vaccine-elicited, fusion... -

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Basic information

Entry
Database: EMDB / ID: EMD-8950
TitleCryo-EM structure at 3.5 A resolution of vaccine-elicited, fusion peptide-directed antibody OPV-d.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
Map dataMap after refinement in cryosparc and post processing in Relion using the tight mask from cryosparc that was autogenerated for FSC autotightening.
Sample
  • Complex: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies OPV21, VRC03 and PGT122.
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAcharya P / Kwong PD
CitationJournal: To Be Published
Title: Cryo-EM structure at 3.5 A resolution of vaccine-elicited, fusion peptide-directed antibody OPV21 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
Authors: Acharya P / Kwong PD
History
DepositionJul 8, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.64
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.64
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8950.png

Downloads & links

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Map

FileDownload / File: emd_8950.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap after refinement in cryosparc and post processing in Relion using the tight mask from cryosparc that was autogenerated for FSC autotightening.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 407.232 Å		1.06 Å/pix.
x 384 pix.
= 407.232 Å		1.06 Å/pix.
x 384 pix.
= 407.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0605 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.64 / Movie #1: 1.64
Minimum - Maximum-1.9246954 - 6.4722576
Average (Standard dev.)0.018950226 (±0.17882414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.232 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06051.06051.0605
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z407.232407.232407.232
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ224224224
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.9256.4720.019

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Supplemental data

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Mask #1

Fileemd_8950_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_8950_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map generated after postprocessing in RELION using the...

Fileemd_8950_additional.map
AnnotationMap generated after postprocessing in RELION using the looser mask generated in CryoSparc (used in the final iteration of cryoSparc refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_8950_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_8950_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of...

EntireName: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies OPV21, VRC03 and PGT122.
Components
  • Complex: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies OPV21, VRC03 and PGT122.

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Supramolecule #1: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of...

SupramoleculeName: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies OPV21, VRC03 and PGT122.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.01
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: SPOTITON

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2700 / Average exposure time: 10.0 sec. / Average electron dose: 95.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 497508
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 90701
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 156

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