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- EMDB-5552: Molecular structure of the native HIV-1 Env trimer bound to m36: ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5552
TitleMolecular structure of the native HIV-1 Env trimer bound to m36: Spike region
Map dataMolecular structure of native HIV-1 Env trimer bound to m36: Spike regions
Sample
  • Sample: m36 in complex with HIV-1 Bal Env
  • Protein or peptide: HIV-1 envelope glycoprotein
Keywordsgp120 / gp41 / cryoelectron microscopy / AIDS vaccine / virus entry
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM
AuthorsMeyerson JR / Tran EEH / Kuybeda O / Chen W / Dimitrov DS / Gorlani A / Verrips T / Lifson JD / Subramaniam S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives.
Authors: Joel R Meyerson / Erin E H Tran / Oleg Kuybeda / Weizao Chen / Dimiter S Dimitrov / Andrea Gorlani / Theo Verrips / Jeffrey D Lifson / Sriram Subramaniam /
Abstract: The extensive carbohydrate coat, the variability of protein structural features on HIV-1 envelope glycoproteins (Env), and the steric constraints of the virus-cell interface during infection, present ...The extensive carbohydrate coat, the variability of protein structural features on HIV-1 envelope glycoproteins (Env), and the steric constraints of the virus-cell interface during infection, present challenges to the elicitation of effective full-length (~150 kDa), neutralizing antibodies against HIV. These hurdles have motivated the engineering of smaller antibody derivatives that can bind Env and neutralize the virus. To further understand the mechanisms by which these proteins neutralize HIV-1, we carried out cryoelectron tomography of native HIV-1 BaL virions complexed separately to two small (~15 kDa) HIV-neutralizing proteins: A12, which binds the CD4-binding site on Env, and m36, whose binding to Env is enhanced by CD4 binding. We show that despite their small size, the presence of these proteins and their effects on the quaternary conformation of trimeric Env can be visualized in molecular structures derived by cryoelectron tomography combined with subvolume averaging. Binding of Env to A12 results in a conformational change that is comparable to changes observed upon its binding to the CD4-binding site antibody, b12. In contrast, binding of Env to m36 results in an "open" quaternary conformation similar to that seen with binding of soluble CD4 or the CD4i antibody, 17b. Because these small neutralizing proteins are less sterically hindered than full-length antibodies at zones of virus-cell contact, the finding that their binding has the same structural consequences as that of other broadly neutralizing antibodies highlights their potential for use in therapeutic applications.
History
DepositionDec 15, 2012-
Header (metadata) releaseJan 9, 2013-
Map releaseJan 9, 2013-
UpdateJan 16, 2013-
Current statusJan 16, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.395
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.395
  • Imaged by UCSF Chimera
  • Download
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_5552.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMolecular structure of native HIV-1 Env trimer bound to m36: Spike regions
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 0.395 / Movie #1: 0.395
Minimum - Maximum-0.00022189 - 1.63900685
Average (Standard dev.)0.0112104 (±0.10717136)
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-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0001.6390.011

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Supplemental data

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Sample components

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Entire : m36 in complex with HIV-1 Bal Env

EntireName: m36 in complex with HIV-1 Bal Env
Components
  • Sample: m36 in complex with HIV-1 Bal Env
  • Protein or peptide: HIV-1 envelope glycoprotein

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Supramolecule #1000: m36 in complex with HIV-1 Bal Env

SupramoleculeName: m36 in complex with HIV-1 Bal Env / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: HIV-1 envelope glycoprotein

MacromoleculeName: HIV-1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: HIV-1 surface spike / Recombinant expression: No / 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

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Sample preparation

BufferDetails: HIV-1 BaL virions in TNE buffer treated with 1 mM Aldrithiol-2, 16mg/mL m36 in PBS buffer, pH 7.4
GridDetails: Quantifoil Multi-A, 200 mesh
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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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 FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 34000
Specialist opticsEnergy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DateJul 11, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 100 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD
DetailsAverage number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.

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