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- EMDB-6540: Structure of Simian Immunodeficiency Virus Envelope Spikes bound ... -

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Entry
Database: EMDB / ID: EMD-6540
TitleStructure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5
Map dataReconstruction of open state SIV envelope spike bound with CD4
Sample
  • Sample: SIV envelope bound to CD4 in open state
  • Virus: Simian immunodeficiency virus
  • Protein or peptide: T-cell surface glycoprotein CD4
KeywordsCryoelectron tomography / image processing / electron microscopy / immunology / AIDS / HIV
Biological speciesHomo sapiens (human) / Simian immunodeficiency virus
Methodsubtomogram averaging / cryo EM
AuthorsHu G / Liu J / Roux KH / Taylor KA
CitationJournal: J Virol / Year: 2017
Title: Structure of Simian Immunodeficiency Virus Envelope Spikes Bound with CD4 and Monoclonal Antibody 36D5.
Authors: Guiqing Hu / Jun Liu / Kenneth H Roux / Kenneth A Taylor /
Abstract: The human immunodeficiency virus type 1 (HIV-1)/simian immunodeficiency virus (SIV) envelope spike (Env) mediates viral entry into host cells. The V3 loop of the gp120 component of the Env trimer ...The human immunodeficiency virus type 1 (HIV-1)/simian immunodeficiency virus (SIV) envelope spike (Env) mediates viral entry into host cells. The V3 loop of the gp120 component of the Env trimer contributes to the coreceptor binding site and is a target for neutralizing antibodies. We used cryo-electron tomography to visualize the binding of CD4 and the V3 loop monoclonal antibody (MAb) 36D5 to gp120 of the SIV Env trimer. Our results show that 36D5 binds gp120 at the base of the V3 loop and suggest that the antibody exerts its neutralization effect by blocking the coreceptor binding site. The antibody does this without altering the dynamics of the spike motion between closed and open states when CD4 is bound. The interaction between 36D5 and SIV gp120 is similar to the interaction between some broadly neutralizing anti-V3 loop antibodies and HIV-1 gp120. Two conformations of gp120 bound with CD4 are revealed, suggesting an intrinsic dynamic nature of the liganded Env trimer. CD4 binding substantially increases the binding of 36D5 to gp120 in the intact Env trimer, consistent with CD4-induced changes in the conformation of gp120 and the antibody binding site. Binding by MAb 36D5 does not substantially alter the proportions of the two CD4-bound conformations. The position of MAb 36D5 at the V3 base changes little between conformations, indicating that the V3 base serves as a pivot point during the transition between these two states. Glycoprotein spikes on the surfaces of SIV and HIV are the sole targets available to the immune system for antibody neutralization. Spikes evade the immune system by a combination of a thick layer of polysaccharide on the surface (the glycan shield) and movement between spike domains that masks the epitope conformation. Using SIV virions whose spikes were "decorated" with the primary cellular receptor (CD4) and an antibody (36D5) at part of the coreceptor binding site, we visualized multiple conformations trapped by the rapid freezing step, which were separated using statistical analysis. Our results show that the CD4-induced conformational dynamics of the spike enhances binding of the antibody.
History
DepositionNov 24, 2015-
Header (metadata) releaseApr 27, 2016-
Map releaseMay 24, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6540.tif

Downloads & links

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Map

FileDownload / File: emd_6540.map.gz / Format: CCP4 / Size: 348.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of open state SIV envelope spike bound with CD4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.7 Å/pix.
x 45 pix.
= 256.5 Å		5.7 Å/pix.
x 45 pix.
= 256.5 Å		5.7 Å/pix.
x 45 pix.
= 256.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-0.97557151 - 2.58905053
Average (Standard dev.)1.00092864 (±0.41012663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-22-22-22
Dimensions454545
Spacing454545
CellA=B=C: 256.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.75.75.7
M x/y/z454545
origin x/y/z0.0000.0000.000
length x/y/z256.500256.500256.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-22-22-22
NC/NR/NS454545
D min/max/mean-0.9762.5891.001

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Supplemental data

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Sample components

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Entire : SIV envelope bound to CD4 in open state

EntireName: SIV envelope bound to CD4 in open state
Components
  • Sample: SIV envelope bound to CD4 in open state
  • Virus: Simian immunodeficiency virus
  • Protein or peptide: T-cell surface glycoprotein CD4

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Supramolecule #1000: SIV envelope bound to CD4 in open state

SupramoleculeName: SIV envelope bound to CD4 in open state / type: sample / ID: 1000 / Oligomeric state: gp120 trimer bound to CD4 in open state / Number unique components: 2

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Supramolecule #1: Simian immunodeficiency virus

SupramoleculeName: Simian immunodeficiency virus / type: virus / ID: 1 / Name.synonym: SIV / NCBI-ID: 11723 / Sci species name: Simian immunodeficiency virus / Sci species strain: SIV239/251tail/Supt-CCR5 CL.30 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: SIV
Host (natural)Organism: Cercopithecidae (Old World monkeys) / synonym: VERTEBRATES

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Macromolecule #1: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 1 / Name.synonym: CD4 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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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: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
DateAug 16, 2008
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 31000
Sample stageSpecimen holder: cryo holder / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: I3, protomo / Number subtomograms used: 2033

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Atomic model buiding 1

Initial modelPDB ID:

4nco

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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