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- EMDB-5680: Cryo-electron microscopy of a trimeric soluble HIV Env construct,... -

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Basic information

Entry
Database: EMDB / ID: EMD-5680
TitleCryo-electron microscopy of a trimeric soluble HIV Env construct, gp140 SOSIP, in complex with Fab Z13e1
Map dataReconstruction of trimeric HIV gp140 with MPER FAB
Sample
  • Sample: Molecular structure of KNH1144 SOSIP gp140 with Z13e1 Fab
  • Protein or peptide: Envelope glycoprotein
  • Protein or peptide: Fab portion of monoclonal antibody Z13e1
KeywordsHIV / gp140 / SOSIP / Z13e1
Biological speciesHuman immunodeficiency virus 1 / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.5 Å
AuthorsHarris AK / Bartesaghi A / Milne JL / Subramaniam S
CitationJournal: J Virol / Year: 2013
Title: HIV-1 envelope glycoprotein trimers display open quaternary conformation when bound to the gp41 membrane-proximal external-region-directed broadly neutralizing antibody Z13e1.
Authors: Audray K Harris / Alberto Bartesaghi / Jacqueline L S Milne / Sriram Subramaniam /
Abstract: We describe cryo-electron microscopic studies of the interaction between the ectodomain of the trimeric HIV-1 envelope glycoprotein (Env) and Z13e1, a broadly neutralizing antibody that targets the ...We describe cryo-electron microscopic studies of the interaction between the ectodomain of the trimeric HIV-1 envelope glycoprotein (Env) and Z13e1, a broadly neutralizing antibody that targets the membrane-proximal external region (MPER) of the gp41 subunit. We show that Z13e1-bound Env displays an open quaternary conformation similar to the CD4-bound conformation. Our results support the idea that MPER-directed antibodies, such as Z13e1, block viral entry by interacting with Env at a step after CD4 activation.
History
DepositionMay 30, 2013-
Header (metadata) releaseAug 21, 2013-
Map releaseAug 21, 2013-
UpdateAug 21, 2013-
Current statusAug 21, 2013Processing 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5680_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5680.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of trimeric HIV gp140 with MPER FAB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 184 pix.
= 248.4 Å		1.35 Å/pix.
x 184 pix.
= 248.4 Å		1.35 Å/pix.
x 184 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-7.80842304 - 7.98503494
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-68-68-68
Dimensions184184184
Spacing184184184
CellA=B=C: 248.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z184184184
origin x/y/z0.0000.0000.000
length x/y/z248.400248.400248.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-68-68-68
NC/NR/NS184184184
D min/max/mean-7.8087.985-0.000

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Supplemental data

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Sample components

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Entire : Molecular structure of KNH1144 SOSIP gp140 with Z13e1 Fab

EntireName: Molecular structure of KNH1144 SOSIP gp140 with Z13e1 Fab
Components
  • Sample: Molecular structure of KNH1144 SOSIP gp140 with Z13e1 Fab
  • Protein or peptide: Envelope glycoprotein
  • Protein or peptide: Fab portion of monoclonal antibody Z13e1

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Supramolecule #1000: Molecular structure of KNH1144 SOSIP gp140 with Z13e1 Fab

SupramoleculeName: Molecular structure of KNH1144 SOSIP gp140 with Z13e1 Fab
type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 2

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Macromolecule #1: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / 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: isolate 00KE_KNH1144 / synonym: HIV-1
Molecular weightExperimental: 420 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: SOSIP-PPI4 and furin-pcDNA3.1

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Macromolecule #2: Fab portion of monoclonal antibody Z13e1

MacromoleculeName: Fab portion of monoclonal antibody Z13e1 / type: protein_or_peptide / ID: 2 / Name.synonym: Z13e1 Fab / Details: Fab fragment / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 50 KDa

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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

Concentration0.42 mg/mL
BufferpH: 7.5 / Details: TNE Buffer (10 mM Tris, 150 mM NaCl, 1 mM EDTA)
GridDetails: Quantifoil, plasma cleaned
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III
Method: Blot for 6 seconds (blot offset -2) and plunge into an ethane slurry cooled by liquid nitrogen.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateAug 31, 2009
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 583 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 80 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 59500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 7050

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Atomic model buiding 1

Initial modelPDB ID:

1gc1

SoftwareName: Chimera
DetailsProtocol: Rigid body. Automated fitting procedures
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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