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- EMDB-5779: Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 ... -

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Entry
Database: EMDB / ID: EMD-5779
TitleCryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs
Map dataCryo-EM structure of a fully glycosylated SOSIP.664 Env trimer with 3 broadly neutralizing PGV04 Fabs
Sample
  • Sample: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs
  • Protein or peptide: BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140
  • Protein or peptide: Fragment antigen bindingFragment antigen-binding
KeywordsHIV-1 trimeric spike / gp140 / SOSIP / broadly neutralizing antibody / PGV04 / Env / Envelope glycoprotein
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsLyumkis D / Julien JP / de Val N / Cupo A / Potter CS / Klasse PJ / Burton DR / Sanders RW / Moore JP / Carragher B ...Lyumkis D / Julien JP / de Val N / Cupo A / Potter CS / Klasse PJ / Burton DR / Sanders RW / Moore JP / Carragher B / Wilson IA / Ward AB
CitationJournal: Science / Year: 2013
Title: Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer.
Authors: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A ...Authors: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A Wilson / Andrew B Ward /
Abstract: The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly ...The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described.
History
DepositionOct 26, 2013-
Header (metadata) releaseNov 13, 2013-
Map releaseNov 13, 2013-
UpdateJan 8, 2014-
Current statusJan 8, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j5m
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5779.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a fully glycosylated SOSIP.664 Env trimer with 3 broadly neutralizing PGV04 Fabs
Voxel sizeX=Y=Z: 1.21 Å
Density
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.02848566 - 0.06708022
Average (Standard dev.)0.00017031 (±0.00453258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 309.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z309.760309.760309.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0280.0670.000

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Supplemental data

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Sample components

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Entire : Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly...

EntireName: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs
Components
  • Sample: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs
  • Protein or peptide: BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140
  • Protein or peptide: Fragment antigen bindingFragment antigen-binding

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Supramolecule #1000: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly...

SupramoleculeName: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs
type: sample / ID: 1000
Oligomeric state: three SOSIP.664 gp140 subunits (trimeric HIV-1 spike) with 3 PGV04 Fabs
Number unique components: 2
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140

MacromoleculeName: BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140 / type: protein_or_peptide / ID: 1 / Name.synonym: Env / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505.W6M.ENV.A5 / synonym: human immunodeficiency virus type I
Molecular weightTheoretical: 600 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T

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Macromolecule #2: Fragment antigen binding

MacromoleculeName: Fragment antigen binding / type: protein_or_peptide / ID: 2 / Name.synonym: Fab / Number of copies: 3 / Oligomeric state: heterodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F

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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

Concentration0.72 mg/mL
BufferpH: 7.6 / Details: 20 mM Tris, 150 mM NaCl, 0.085 mM DDM
GridDetails: 400 mesh C-Flat CF-22-4C, plasma treated for 5 seconds
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Method: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 ...Method: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 seconds, followed by blotting with a small piece of filter paper and plunge-freezing into liquid ethane using a manual cryo-plunger in an ambient environment (4 degrees C).

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected by observing Thon rings with the Leginon software
Detailselectron counting mode
DateFeb 21, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 6355 / Average electron dose: 32 e/Å2
Details: The dose was fractionated over 20 raw frames collected over a 5-second exposure time (250 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~9. ...Details: The dose was fractionated over 20 raw frames collected over a 5-second exposure time (250 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~9.4 e-/pixel/sec. The individual frames were aligned using a GPU-enabled frame-alignment program that was generously provided by Yifan Cheng and Xueming Li. This program was used to track the global shifts between individual frames.
Tilt angle min0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Frealign
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Xmipp, Frealign
Details: Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers.
Number images used: 49572
DetailsReconstructed using resolution-limited refinement procedure implemented in Xmipp and Frealign.

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Atomic model buiding 1

Initial modelPDB ID:
RefinementSpace: REAL
Output model

PDB-3j5m:
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs

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Atomic model buiding 2

Initial modelPDB ID:
RefinementSpace: REAL
Output model

PDB-3j5m:
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs

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Atomic model buiding 3

Initial modelPDB ID:
RefinementSpace: REAL
Output model

PDB-3j5m:
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs

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Atomic model buiding 4

Initial modelPDB ID:
RefinementSpace: REAL
Output model

PDB-3j5m:
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs

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