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- EMDB-5325: Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5325
TitleMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
Map dataMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
Sample
  • Sample: SOSIP gp140 KNH1144 17b
  • Protein or peptide: SOSIP gp140 KNH1144 17b
KeywordsHIV/AIDS vaccine / immunogen / HIV glycoprotein structure / gp140 trimer / cryo-electron tomography / sub-tomogram averaging / cryo-electron microscopy
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsHarris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW ...Harris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW / Klasse PJ / Milne JL / Wilson IA / Olson WC / Moore JP / Subramaniam S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
Authors: Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / ...Authors: Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / Jacqueline L S Milne / Ian A Wilson / William C Olson / John P Moore / Sriram Subramaniam /
Abstract: The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface ...The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). The design of soluble versions of trimeric Env that display structural and functional properties similar to those observed on intact viruses is highly desirable from the viewpoint of designing immunogens that could be effective as vaccines against HIV/AIDS. Using cryoelectron tomography combined with subvolume averaging, we have analyzed the structure of SOSIP gp140 trimers, which are cleaved, solubilized versions of the ectodomain of trimeric HIV-1 Env. We show that unliganded gp140 trimers adopt a quaternary arrangement similar to that displayed by native unliganded trimers on the surface of intact HIV-1 virions. When complexed with soluble CD4, Fab 17b, which binds to gp120 at its chemokine coreceptor binding site, or both soluble CD4 and 17b Fab, gp140 trimers display an open conformation in which there is an outward rotation and displacement of each gp120 protomer. We demonstrate that the molecular arrangements of gp120 trimers in the closed and open conformations of the soluble trimer are the same as those observed for the closed and open states, respectively, of trimeric gp120 on intact HIV-1 BaL virions, establishing that soluble gp140 trimers can be designed to mimic the quaternary structural transitions displayed by native trimeric Env.
History
DepositionJul 11, 2011-
Header (metadata) releaseMay 31, 2012-
Map releaseMay 31, 2012-
UpdateMay 31, 2012-
Current statusMay 31, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5325_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5325.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.37717438 - 8.505661010000001
Average (Standard dev.)-0.00243358 (±0.6463089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-6.3778.506-0.002

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Supplemental data

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Sample components

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Entire : SOSIP gp140 KNH1144 17b

EntireName: SOSIP gp140 KNH1144 17b
Components
  • Sample: SOSIP gp140 KNH1144 17b
  • Protein or peptide: SOSIP gp140 KNH1144 17b

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Supramolecule #1000: SOSIP gp140 KNH1144 17b

SupramoleculeName: SOSIP gp140 KNH1144 17b / type: sample / ID: 1000 / Oligomeric state: trimeric / Number unique components: 4

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Macromolecule #1: SOSIP gp140 KNH1144 17b

MacromoleculeName: SOSIP gp140 KNH1144 17b / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Human immunodeficiency virus 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding 1

Initial modelPDB ID:

3dno

SoftwareName: Chimera
RefinementSpace: REAL

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