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- EMDB-27631: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin -

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Basic information

Entry
Database: EMDB / ID: EMD-27631
TitleSIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin
Map data
Sample
  • Complex: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin
Biological speciesArtocarpus heterophyllus (jackfruit)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.64 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSimons Foundation (SF349247) United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Cryo-EM structures of prefusion SIV envelope trimer.
Authors: Jason Gorman / Chunyan Wang / Rosemarie D Mason / Alexandra F Nazzari / Hugh C Welles / Tongqing Zhou / Julian W Bess / Tatsiana Bylund / Myungjin Lee / Yaroslav Tsybovsky / Raffaello ...Authors: Jason Gorman / Chunyan Wang / Rosemarie D Mason / Alexandra F Nazzari / Hugh C Welles / Tongqing Zhou / Julian W Bess / Tatsiana Bylund / Myungjin Lee / Yaroslav Tsybovsky / Raffaello Verardi / Shuishu Wang / Yongping Yang / Baoshan Zhang / Reda Rawi / Brandon F Keele / Jeffrey D Lifson / Jun Liu / Mario Roederer / Peter D Kwong /
Abstract: Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion ...Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion stabilization and cryo-EM structures of soluble envelope (Env) trimers from rhesus macaque SIV (SIV) in complex with neutralizing antibodies. These structures provide residue-level definition for SIV-specific disulfide-bonded variable loops (V1 and V2), which we used to delineate variable-loop coverage of the Env trimer. The defined variable loops enabled us to investigate assembled Env-glycan shields throughout SIV, which we found to comprise both N- and O-linked glycans, the latter emanating from V1 inserts, which bound the O-link-specific lectin jacalin. We also investigated in situ SIV-Env trimers on virions, determining cryo-electron tomography structures at subnanometer resolutions for an antibody-bound complex and a ligand-free state. Collectively, these structures define the prefusion-closed structure of the SIV-Env trimer and delineate variable-loop and glycan-shielding mechanisms of immune evasion conserved throughout SIV evolution.
History
DepositionJul 15, 2022-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27631.png

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Map

FileDownload / File: emd_27631.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 210 pix.
= 454.86 Å		2.17 Å/pix.
x 210 pix.
= 454.86 Å		2.17 Å/pix.
x 210 pix.
= 454.86 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.166 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.3349107 - 1.7569388
Average (Standard dev.)0.002185474 (±0.07340241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 454.86 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27631_msk_1.map
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Half map: #1

Fileemd_27631_half_map_1.map
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Half map: #2

Fileemd_27631_half_map_2.map
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Sample components

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Entire : SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin

EntireName: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin
Components
  • Complex: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin

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Supramolecule #1: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin

SupramoleculeName: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Artocarpus heterophyllus (jackfruit)

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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

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsSIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 52.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 8589
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3)

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