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- EMDB-28910: Glycan-Base ConC Env Trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-28910
TitleGlycan-Base ConC Env Trimer
Map dataMap from Non-Uniform Refinement
Sample
  • Complex: HIV-1 Consensus C Env trimer with glycan covered base
    • Protein or peptide: HIV-1 Env gp41
    • Protein or peptide: HIV-1 Env gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Glycan / Env / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsOlia AS / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: iScience / Year: 2023
Title: Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases.
Authors: Adam S Olia / Cheng Cheng / Tongqing Zhou / Andrea Biju / Darcy R Harris / Anita Changela / Hongying Duan / Vera B Ivleva / Wing-Pui Kong / Li Ou / Reda Rawi / Yaroslav Tsybovsky / David J ...Authors: Adam S Olia / Cheng Cheng / Tongqing Zhou / Andrea Biju / Darcy R Harris / Anita Changela / Hongying Duan / Vera B Ivleva / Wing-Pui Kong / Li Ou / Reda Rawi / Yaroslav Tsybovsky / David J Van Wazer / Angela R Corrigan / Christopher A Gonelli / Myungjin Lee / Krisha McKee / Sandeep Narpala / Sijy O'Dell / Danealle K Parchment / Erik-Stephane D Stancofski / Tyler Stephens / Ivy Tan / I-Ting Teng / Shuishu Wang / Qing Wei / Yongping Yang / Zhengrong Yang / Baoshan Zhang / / Jan Novak / Matthew B Renfrow / Nicole A Doria-Rose / Richard A Koup / Adrian B McDermott / Jason G Gall / Q Paula Lei / John R Mascola / Peter D Kwong /
Abstract: Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess ...Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential -linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response.
History
DepositionNov 20, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28910.png

Downloads & links

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Map

FileDownload / File: emd_28910.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap from Non-Uniform Refinement
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.11969909 - 0.26305935
Average (Standard dev.)0.00094155135 (±0.011219491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28910_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A from Non-Uniform Refinement

Fileemd_28910_half_map_1.map
AnnotationHalf-map A from Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B from Non-Uniform Refinement

Fileemd_28910_half_map_2.map
AnnotationHalf-map B from Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Consensus C Env trimer with glycan covered base

EntireName: HIV-1 Consensus C Env trimer with glycan covered base
Components
  • Complex: HIV-1 Consensus C Env trimer with glycan covered base
    • Protein or peptide: HIV-1 Env gp41
    • Protein or peptide: HIV-1 Env gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Consensus C Env trimer with glycan covered base

SupramoleculeName: HIV-1 Consensus C Env trimer with glycan covered base / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 Env gp41

MacromoleculeName: HIV-1 Env gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.547807 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTAVPW NSTWSNKTQE DIWDNMTWMQ WDREISNYTD TIYRLLEESQ FQQEINEKDN LTLPNST

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Macromolecule #2: HIV-1 Env gp120

MacromoleculeName: HIV-1 Env gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.495898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NSTAENLWVT VYYGVPVWKE AKTTLFCASD AKAYEKEVHN VWATHACVPT DPNPQEMVLE NVTENFNMWK NDMVDQMHED IISLWDQSL KPCVKLTPLC VTLNCTNVNV TNTNNNNMKE EMKNCSFNTT TEIRDKKQKE YALFYRLDIV PLNENSSEYR L INCNTSTC ...String:
NSTAENLWVT VYYGVPVWKE AKTTLFCASD AKAYEKEVHN VWATHACVPT DPNPQEMVLE NVTENFNMWK NDMVDQMHED IISLWDQSL KPCVKLTPLC VTLNCTNVNV TNTNNNNMKE EMKNCSFNTT TEIRDKKQKE YALFYRLDIV PLNENSSEYR L INCNTSTC TQICPKVSFD PIPIHYCAPA GYAILKCNNK TFNGTGPCNN VSTVQCTHGI KPVVSTQLLL NGSLAEEEII IR SENLTDN AKTIIVHLNE SVEINCTRPN NMTRKSIRIG PGQTFYALGD IIGDIRQPHC NISEAKWNKT LQRVKKKLKE HFP NKTIKF APSSGGDLEI TTHSFNCRGE FFYCNTSKLF NSTYNNTTSN STITLPCRIK QIINMWQEVG RCMYAPPIAG NITC KSNIT GLLLTRDGGN NNNNTETFRP GGGDMRDNWR SELYKYKVVE IKPLGIAPTK CNRTVVENST HKNLTHHMRR RRRR

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.54 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ck9

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12967

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