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- EMDB-40853: CH505 Disulfide Stapled SOSIP Bound to b12 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-40853
TitleCH505 Disulfide Stapled SOSIP Bound to b12 Fab
Map dataCH505 Disulfide Stapled SOSIP Bound to CH235.12 Fab
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: HIV-1 gp41
    • Protein or peptide: b12 Heavy Chain
    • Protein or peptide: b12 Light Chain
KeywordsHIV-1 / Envelope / Env / Ectodomain / Fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma 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: 4.5 Å
AuthorsHenderson R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2024
Title: Microsecond dynamics control the HIV-1 Envelope conformation.
Authors: Ashley L Bennett / Robert Edwards / Irina Kosheleva / Carrie Saunders / Yishak Bililign / Ashliegh Williams / Pimthada Bubphamala / Katayoun Manosouri / Kara Anasti / Kevin O Saunders / S ...Authors: Ashley L Bennett / Robert Edwards / Irina Kosheleva / Carrie Saunders / Yishak Bililign / Ashliegh Williams / Pimthada Bubphamala / Katayoun Manosouri / Kara Anasti / Kevin O Saunders / S Munir Alam / Barton F Haynes / Priyamvada Acharya / Rory Henderson /
Abstract: The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the ...The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.
History
DepositionMay 22, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40853.png

Downloads & links

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Map

FileDownload / File: emd_40853.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCH505 Disulfide Stapled SOSIP Bound to CH235.12 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 262.2 Å		0.87 Å/pix.
x 300 pix.
= 262.2 Å		0.87 Å/pix.
x 300 pix.
= 262.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.874 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.194
Minimum - Maximum-0.5081489 - 0.72787035
Average (Standard dev.)0.0012279722 (±0.02765848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 262.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40853_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_40853_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_40853_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 : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: HIV-1 gp41
    • Protein or peptide: b12 Heavy Chain
    • Protein or peptide: b12 Light Chain

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: SUBSPECIES / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.446805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNIWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCCTLN CTNATASNSS IIEGMKNCSF NITTELRCKR EKKNALFYKL DIVQLDGNSS QYRLINCDTS V ITQVCPKL ...String:
ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNIWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCCTLN CTNATASNSS IIEGMKNCSF NITTELRCKR EKKNALFYKL DIVQLDGNSS QYRLINCDTS V ITQVCPKL SFDPIPIHYC APAGYAILKC NNKTFTGTGP CNNVSTVQCT HGIKPVLSTQ LLLNGSLAEG EIIIRSENIT KN VKTIIVH LNESVKIECT RPNNKTRTSI RIGPGQAFYA TGQVIGDIRE AYCNINESKW NETLQRVSKK LKEYFPHKNI TFQ PSSGGD LEITTHSFNC GGEFFYCNTS SLFNRTYMAN STETNSTRTI TIHCRIKQII NMWQEVGRAM YAPPIAGNIT CISN ITGLL LTRDYGKNNT ETFRPGGGNM KDNWRSELYK YKVVKIEPLG VAPTRCKRRV V

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: HIV-1 gp41

MacromoleculeName: HIV-1 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 14.265115 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VFLGFLGAAG STMGAASMTL TVQARNLLSG TVWGIKQLQA RVLAVERYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMT WLQWDKEISN YTQIIYGLLE ESQNQQEKNE QDLLALD

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Macromolecule #3: b12 Heavy Chain

MacromoleculeName: b12 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 14.370952 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCQASGYRFS NFVIHWVRQA PGQRFEWMGW INPYNGNKEF SAKFQDRVTF TADTSANTAY MELRSLRSA DTAVYYCARV GPYSWDDSPQ DNYYMDVWGK GTTVIVSS

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Macromolecule #4: b12 Light Chain

MacromoleculeName: b12 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 11.877216 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT FSCRSSHSIR SRRVAWYQHK PGQAPRLVIH GVSNRASGIS DRFSGSGSGT DFTLTITRVE PEDFALYYC QVYGASSYTF GQGTKLERK

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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: 7.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.48 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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