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- EMDB-41246: Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus niv... -

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Basic information

Entry
Database: EMDB / ID: EMD-41246
TitleCryo-EM structure of 1059 SOSIP trimer purified via Galanthus nivalis lectin chromatography
Map data
Sample
  • Complex: Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus nivalis lectin chromatography
    • Protein or peptide: 1059 SOSIP Surface protein gp120
    • Protein or peptide: 1059 SOSIP Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Glycoprotein / Lectin / Trimer / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsParsons RJ / Pothula K / Acharya P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170752 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01 AI169587 United States
CitationJournal: Nat Commun / Year: 2024
Title: Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/founder sensitivity to broadly neutralizing antibodies.
Authors: Durgadevi Parthasarathy / Karunakar Reddy Pothula / Sneha Ratnapriya / Héctor Cervera Benet / Ruth Parsons / Xiao Huang / Salam Sammour / Katarzyna Janowska / Miranda Harris / Joseph ...Authors: Durgadevi Parthasarathy / Karunakar Reddy Pothula / Sneha Ratnapriya / Héctor Cervera Benet / Ruth Parsons / Xiao Huang / Salam Sammour / Katarzyna Janowska / Miranda Harris / Joseph Sodroski / Priyamvada Acharya / Alon Herschhorn /
Abstract: HIV-1 envelope glycoproteins (Envs) of most primary HIV-1 strains exist in closed conformation and infrequently sample open states, limiting access to internal epitopes. Thus, immunogen design aims ...HIV-1 envelope glycoproteins (Envs) of most primary HIV-1 strains exist in closed conformation and infrequently sample open states, limiting access to internal epitopes. Thus, immunogen design aims to mimic the closed Env conformation as preferred target for eliciting broadly neutralizing antibodies (bnAbs). Here we identify incompletely closed Env conformations of 6 out of 13 transmitted/founder (T/F) strains that are sensitive to antibodies that recognize internal epitopes typically exposed on open Envs. A 3.6 Å cryo-electron microscopy structure of unliganded, incompletely closed T/F Envs (1059-SOSIP) reveals protomer motion that increased sampling of states with incompletely closed trimer apex. We reconstruct de novo the post-transmission evolutionary pathway of a second T/F. Evolved viruses exhibit increased Env resistance to cold, soluble CD4 and 19b, all of which correlate with closing of the adapted Env trimer. Lastly, we show that the ultra-broad N6 bnAb efficiently recognizes different Env conformations and exhibits improved antiviral breadth against VRC01-resistant Envs isolated during the first-in-humans antibody-mediated-prevention trial.
History
DepositionJul 13, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41246.png

Downloads & links

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Map

FileDownload / File: emd_41246.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.4690934 - 2.1104517
Average (Standard dev.)0.00024229178 (±0.04223845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus niv...

EntireName: Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus nivalis lectin chromatography
Components
  • Complex: Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus nivalis lectin chromatography
    • Protein or peptide: 1059 SOSIP Surface protein gp120
    • Protein or peptide: 1059 SOSIP Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus niv...

SupramoleculeName: Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus nivalis lectin chromatography
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 217.5 KDa

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Macromolecule #1: 1059 SOSIP Surface protein gp120

MacromoleculeName: 1059 SOSIP Surface protein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 55.390684 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEQLWVTVYY GVPVWKEATT TLFCASDAKA YTAEAHNVWA THACVPTDPN PQEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL NCTDLANNTN LANNTNSSIS SWEKMEKGEI KNCSFNITTV IKDKIQKNYA LFNRLDIVPI D DDDTNVTN ...String:
AEQLWVTVYY GVPVWKEATT TLFCASDAKA YTAEAHNVWA THACVPTDPN PQEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL NCTDLANNTN LANNTNSSIS SWEKMEKGEI KNCSFNITTV IKDKIQKNYA LFNRLDIVPI D DDDTNVTN NASYRLISCN TSVITQACPK ISFEPIPIHY CAPAGFAILK CNDKKFNGTG PCTNVSTVQC THGIKPVVST QL LLNGSLA EEEVVIRSEN FTDNVKTIIV QLNESVIINC TRPNNNTRKS ITFGPGRAFY TTGDIIGDIR KAYCNISSTQ WNN TLRQIA RRLREQFKDK TIVFNSSSGG DPEIVMHSFN CGGEFFYCNT TQLFNSTWNG NDTGEFNNTG KNITYITLPC RIKQ IINMW QEVGKAMYAP PIAGQIRCSS NITGILLTRD GGNSSEDKEI FRPEGGNMRD NWRSELYKYK VVKIEPLGVA PTKCK RRVV QRRRRRR

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Macromolecule #2: 1059 SOSIP Transmembrane protein gp41

MacromoleculeName: 1059 SOSIP Transmembrane protein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.258609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RLLLSGIVQQ QNNLLRAPEA QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICCTAVPW NASWSNRSLD NIWNNMTWME WDREINNYTN LIYNLIEESQ NQQEKNEQEL LELD

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 11 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 8
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP / Details: Leica EM GP2.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe data were processed in cryoSPARCv4.01. Movies were aligned using Patch Motion Correction and the non-dose weighted aligned micrographs were used for the CTF correction with PatchCTF Estimation.
Particle selectionNumber selected: 7260519
Details: In the first round of particle selection, particles were picked with a box size of 280 angstroms using the Blob picker with a circular blob having a maximum diameter of 240 angstroms and ...Details: In the first round of particle selection, particles were picked with a box size of 280 angstroms using the Blob picker with a circular blob having a maximum diameter of 240 angstroms and these particles were subjected to multiple rounds of 2D classification.
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 737588
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.01)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7lx2


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT / Overall B value: 51.14
Output model

PDB-8tgw:
Cryo-EM structure of 1059 SOSIP trimer purified via Galanthus nivalis lectin chromatography

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