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- EMDB-5263: Quaternary structures of HIV Env immunogen exhibit conformational... -

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Basic information

Entry
Database: EMDB / ID: EMD-5263
TitleQuaternary structures of HIV Env immunogen exhibit conformational vicissitudes and interface diminution elicited by ligand binding
Map datagp140
Sample
  • Sample: o-gp140dV2TV1 trimer
  • Protein or peptide: o-gp140dV2TV1
KeywordsHIV-1 / Env trimer / cryoelectron microscopy / induced conformation
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsMoscoso CG / Sun Y / Poon S / Xing L / Kan E / Martin L / Green DJ / Lin F / Vahlne A / Barnett SW ...Moscoso CG / Sun Y / Poon S / Xing L / Kan E / Martin L / Green DJ / Lin F / Vahlne A / Barnett SW / Srivastava IK / Cheng RH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Quaternary structures of HIV Env immunogen exhibit conformational vicissitudes and interface diminution elicited by ligand binding.
Authors: Carlos G Moscoso / Yide Sun / Selina Poon / Li Xing / Elaine Kan / Loïc Martin / Dominik Green / Frank Lin / Anders G Vahlne / Susan Barnett / Indresh Srivastava / R Holland Cheng /
Abstract: The human immunodeficiency virus envelope protein is the key element mediating entry into host cells. Conformational rearrangement of Env upon binding to the host CD4 receptor and chemokine ...The human immunodeficiency virus envelope protein is the key element mediating entry into host cells. Conformational rearrangement of Env upon binding to the host CD4 receptor and chemokine coreceptor drives membrane fusion. We elucidated the quaternary arrangement of the soluble Env trimeric immunogen o-gp140ΔV2TV1, in both its native (unliganded) and CD4-induced (liganded) states by cryoelectron microscopy and molecular modeling. The liganded conformation was elicited by binding gp140 to the synthetic CD4-mimicking miniprotein CD4m. Upon CD4m binding, an outward domain shift of the three gp120 subunits diminishes gp120-gp41 interactions, whereas a "flat open" concave trimer apex is observed consequent to gp120 tilting away from threefold axis, likely juxtaposing the fusion peptide with the host membrane. Additional features observed in the liganded conformation include rotations of individual gp120 subunits that may release gp41 for N- and C-helix refolding and also may lead to optimal exposure of the elicited coreceptor binding site. Such quaternary arrangements of gp140 lead to the metastable liganded conformation, with putative locations of exposed epitopes contributing to a description of sequential events occurring prior to membrane fusion. Our observations imply a mechanism whereby a soluble Env trimeric construct, as opposed to trimers extracted from virions, may better expose crucial epitopes such as the CD4 binding site and V3, as well as epitopes in the vicinity of gp41, subsequent to conjugation with CD4m. Structural features gleaned from our studies should aid the design of Env-based immunogens for inducement of potent broadly neutralizing antibodies against exposed conformational epitopes.
History
DepositionFeb 23, 2011-
Header (metadata) releaseMar 14, 2011-
Map releaseMar 5, 2012-
UpdateMar 5, 2012-
Current statusMar 5, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5263_1.tif

Downloads & links

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Map

FileDownload / File: emd_5263.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgp140
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 150 pix.
= 187.5 Å		1.25 Å/pix.
x 150 pix.
= 187.5 Å		1.25 Å/pix.
x 150 pix.
= 187.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1.2
Minimum - Maximum0.0 - 11.99527836
Average (Standard dev.)0.15970545 (±0.7715857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 187.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z187.500187.500187.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean0.00011.9950.160

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Supplemental data

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Sample components

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Entire : o-gp140dV2TV1 trimer

EntireName: o-gp140dV2TV1 trimer
Components
  • Sample: o-gp140dV2TV1 trimer
  • Protein or peptide: o-gp140dV2TV1

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Supramolecule #1000: o-gp140dV2TV1 trimer

SupramoleculeName: o-gp140dV2TV1 trimer / type: sample / ID: 1000 / Oligomeric state: Trimer / Number unique components: 1
Molecular weightExperimental: 450 KDa / Theoretical: 450 KDa / Method: Triple detector array system

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Macromolecule #1: o-gp140dV2TV1

MacromoleculeName: o-gp140dV2TV1 / type: protein_or_peptide / ID: 1 / Name.synonym: gp140 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / synonym: HIV-1
Molecular weightExperimental: 450 KDa / Theoretical: 450 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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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

Concentration0.1 mg/mL
BufferpH: 7.9 / Details: 20 mM Tris, 50 mM NaCl
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 93 K / Instrument: REICHERT-JUNG PLUNGER / Details: Vitrification instrument: Reichert plunger / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureAverage: 100 K
DateJul 23, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 15 µm / Number real images: 101 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using a semiautomated selection protocol
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 4500
Final angle assignmentDetails: EMAN:alt 90 degrees, az 90 degrees
Final two d classificationNumber classes: 65

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Atomic model buiding 1

Initial modelPDB ID:

2bf1


Chain - Chain ID: A
SoftwareName: SITUS
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. The coordinates were initially manually fitted using program Chimera and refined using program SITUS
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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