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- EMDB-41244: Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus ni... -

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Basic information

Entry
Database: EMDB / ID: EMD-41244
TitleCryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography
Map dataBG505.DS.SOSIP refined map
Sample
  • Complex: Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography
    • Protein or peptide: HIV-1 Envelope glycoprotein BG505 SOSIP
  • 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: 3.8 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41244.png

Downloads & links

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Map

FileDownload / File: emd_41244.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBG505.DS.SOSIP refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 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-1.4333228 - 1.9687288
Average (Standard dev.)0.00012367795 (±0.032175392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 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 BG505 SOSIP trimer purified via Galanthus ni...

EntireName: Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography
Components
  • Complex: Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography
    • Protein or peptide: HIV-1 Envelope glycoprotein BG505 SOSIP
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus ni...

SupramoleculeName: Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 217.5 KDa

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Macromolecule #1: HIV-1 Envelope glycoprotein BG505 SOSIP

MacromoleculeName: HIV-1 Envelope glycoprotein BG505 SOSIP / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 70.900469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LWVTVYYGVP VWKDAETTLF CASDAKAYET EKHNVWATHA CVPTDPNPQE IHLENVTEEF NMWKNNMVEQ MHTDIISLWD QSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR L INCNTSAC ...String:
LWVTVYYGVP VWKDAETTLF CASDAKAYET EKHNVWATHA CVPTDPNPQE IHLENVTEEF NMWKNNMVEQ MHTDIISLWD QSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR L INCNTSAC TQACPKVSFE PIPIHYCAPA GFAILKCKDK KFNGTGPCPS VSTVQCTHGI KPVVSTQLLL NGSLAEEEVM IR SENITNN AKNILVQFNT PVQINCTRPN NNTRKSIRIG PGQAFYATGD IIGDIRQAHC NVSKATWNET LGKVVKQLRK HFG NNTIIR FANSSGGDLE VTTHSFNCGG EFFYCNTSGL FNSTWISNTS VQGSNSTGSN DSITLPCRIK QIINMWQRIG QCMY APPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRRVVGRRR RRRAV GIGA VFLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLR APEAQQHLLK LTVWGIKQLQ ARVLAVERYL RDQQLL GIW GCSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 25 / 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 R1.2/1.3 / 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: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 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: 6566700
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: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 975399
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:

4zmj


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8tgu:
Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography

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