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- EMDB-8629: Conformational states of a soluble, uncleaved HIV-1 envelope trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-8629
TitleConformational states of a soluble, uncleaved HIV-1 envelope trimer
Map dataclass1 (close conformation)
Sample
  • Complex: HIV-1 envelope glycoprotein gp140
    • Protein or peptide: HIV-1 envelope glycoprotein gp140
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / 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: 21.0 Å
AuthorsLiu YH / Pan JH / Cai YF / Grigorieff N / Harrison SC / Chen B
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI084794, AI089618, AI106488, AI112489, AI100645 United States
Howard Hughes Medical Institute (HHMI) United States
Bill & Melinda Gates FoundationOPP1040741 United States
CitationJournal: J Virol / Year: 2017
Title: Conformational States of a Soluble, Uncleaved HIV-1 Envelope Trimer.
Authors: Yuhang Liu / Junhua Pan / Yongfei Cai / Nikolaus Grigorieff / Stephen C Harrison / Bing Chen /
Abstract: The HIV-1 envelope spike [Env; trimeric (gp160) cleaved to (gp120/gp41)] induces membrane fusion, leading to viral entry. It is also the viral component targeted by neutralizing antibodies. Vaccine ...The HIV-1 envelope spike [Env; trimeric (gp160) cleaved to (gp120/gp41)] induces membrane fusion, leading to viral entry. It is also the viral component targeted by neutralizing antibodies. Vaccine development requires production, in quantities suitable for clinical studies, of a recombinant form that resembles functional Env. HIV-1 gp140 trimers-the uncleaved ectodomains of (gp160)-from a few selected viral isolates adopt a compact conformation with many antigenic properties of native Env spikes. One is currently being evaluated in a clinical trial. We report here low-resolution (20 Å) electron cryomicroscopy (cryoEM) structures of this gp140 trimer, which adopts two principal conformations, one closed and the other slightly open. The former is indistinguishable at this resolution from those adopted by a stabilized, cleaved trimer (SOSIP) or by a membrane-bound Env trimer with a truncated cytoplasmic tail (EnvΔCT). The latter conformation is closer to a partially open Env trimer than to the fully open conformation induced by CD4. These results show that a stable, uncleaved HIV-1 gp140 trimer has a compact structure close to that of native Env. Development of any HIV vaccine with a protein component (for either priming or boosting) requires production of a recombinant form to mimic the trimeric, functional HIV-1 envelope spike in quantities suitable for clinical studies. Our understanding of the envelope structure has depended in part on a cleaved, soluble trimer, known as SOSIP.664, stabilized by several modifications, including an engineered disulfide. This construct, which is difficult to produce in large quantities, has yet to induce better antibody responses than those to other envelope-based immunogens, even in animal models. The uncleaved ectodomain of the envelope protein, called gp140, has also been made as a soluble form to mimic the native Env present on the virion surface. Most HIV-1 gp140 preparations are not stable, however, and have an inhomogeneous conformation. The results presented here show that gp140 preparations from suitable isolates can adopt a compact, native-like structure, supporting its use as a vaccine candidate.
History
DepositionFeb 28, 2017-
Header (metadata) releaseMar 8, 2017-
Map releaseMar 8, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8629.png

Downloads & links

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Map

FileDownload / File: emd_8629.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationclass1 (close conformation)
Voxel sizeX=Y=Z: 3.96 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.13682505 - 1.8125496
Average (Standard dev.)-0.016044373 (±0.034623753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 712.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.963.963.96
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z712.800712.800712.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1371.813-0.016

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Supplemental data

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Sample components

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Entire : HIV-1 envelope glycoprotein gp140

EntireName: HIV-1 envelope glycoprotein gp140
Components
  • Complex: HIV-1 envelope glycoprotein gp140
    • Protein or peptide: HIV-1 envelope glycoprotein gp140

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Supramolecule #1: HIV-1 envelope glycoprotein gp140

SupramoleculeName: HIV-1 envelope glycoprotein gp140 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: C97ZA012
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T

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Macromolecule #1: HIV-1 envelope glycoprotein gp140

MacromoleculeName: HIV-1 envelope glycoprotein gp140 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVRGIQRNC QHLWRWGTLI LGMLMICSAA ENLWVGNMWV TVYYGVPVWT DAKTTLFCAS DTKAYDREVH NVWATHACVP TDPNPQEIVL ENVTENFNMW KNDMVDQMHE DIISLWDQSL KPCVKLTPLC VTLHCTNATF KNNVTNDMNK EIRNCSFNTT TEIRDKKQQG ...String:
MRVRGIQRNC QHLWRWGTLI LGMLMICSAA ENLWVGNMWV TVYYGVPVWT DAKTTLFCAS DTKAYDREVH NVWATHACVP TDPNPQEIVL ENVTENFNMW KNDMVDQMHE DIISLWDQSL KPCVKLTPLC VTLHCTNATF KNNVTNDMNK EIRNCSFNTT TEIRDKKQQG YALFYRPDIV LLKENRNNSN NSEYILINCN ASTITQACPK VNFDPIPIHY CAPAGYAILK CNNKTFSGKG PCNNVSTVQC THGIKPVVST QLLLNGSLAE KEIIIRSENL TDNVKTIIVH LNKSVEIVCT RPNNNTRKSM RIGPGQTFYA TGDIIGDIRQ AYCNISGSKW NETLKRVKEK LQENYNNNKT IKFAPSSGGD LEITTHSFNC RGEFFYCNTT RLFNNNATED ETITLPCRIK QIINMWQGVG RAMYAPPIAG NITCKSNITG LLLVRDGGED NKTEEIFRPG GGNMKDNWRS ELYKYKVIEL KPLGIAPTGA KRRVVEREKR AVGIGAVFLG FLGAAGSTMG AASLTLTVQA RQLLSSIVQQ QSNLLRAIEA QQHMLQLTVW GIKQLQTRVL AIERYLKDQQ LLGIWGCSGK LICTTNVPWN SSWSNKSQTD IWNNMTWMEW DREISNYTDT IYRLLEDSQT QQEKNEKDLL ALDSWKNLWS WFDISNWLWY IKSRMKQIED KIEEILSKIY HIENEIARIK KLIGSGGYIP EAPRDGQAYV RKDGEWVLLS TFLGGSGRMK QIEDKIEEIE SKQKKIENEI ARIKKLGSGH HHHHH

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 3138 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2 / Details: movies were collected in super resolution mode
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: OTHER / Details: rosette method described in the paper
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final 3D classificationNumber classes: 6 / Avg.num./class: 17000 / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 17000
FSC plot (resolution estimation)

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