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- EMDB-3059: ZM197 SOSIP.664 trimer in complex with VRC01 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-3059
TitleZM197 SOSIP.664 trimer in complex with VRC01 Fab
Map dataSingle particle reconstruction of the ZM197 SOSIP + VRC01 Fab complex.
Sample
  • Sample: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer
  • Protein or peptide: HIV-1 Env
  • Protein or peptide: VRC01 Antibody
KeywordsHIV-1 / Env / antibody / broadly neutralizing antibodies
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: 9.32 Å
AuthorsLee JH / Ward AB
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens.
Authors: Jean-Philippe Julien / Jeong Hyun Lee / Gabriel Ozorowski / Yuanzi Hua / Alba Torrents de la Peña / Steven W de Taeye / Travis Nieusma / Albert Cupo / Anila Yasmeen / Michael Golabek / ...Authors: Jean-Philippe Julien / Jeong Hyun Lee / Gabriel Ozorowski / Yuanzi Hua / Alba Torrents de la Peña / Steven W de Taeye / Travis Nieusma / Albert Cupo / Anila Yasmeen / Michael Golabek / Pavel Pugach / P J Klasse / John P Moore / Rogier W Sanders / Andrew B Ward / Ian A Wilson /
Abstract: A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 ...A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1.
History
DepositionJun 21, 2015-
Header (metadata) releaseJul 1, 2015-
Map releaseSep 30, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3059.png

emd_3059.png

Downloads & links

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Map

FileDownload / File: emd_3059.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle reconstruction of the ZM197 SOSIP + VRC01 Fab complex.
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.01488768 - 0.05336612
Average (Standard dev.)0.00020703 (±0.00376369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0150.0530.000

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Supplemental data

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Sample components

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Entire : Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer

EntireName: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer
Components
  • Sample: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer
  • Protein or peptide: HIV-1 Env
  • Protein or peptide: VRC01 Antibody

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Supramolecule #1000: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer

SupramoleculeName: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer
type: sample / ID: 1000
Oligomeric state: Each VRC01 Fab binds a gp120 on the trimer
Number unique components: 2
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: HIV-1 Env

MacromoleculeName: HIV-1 Env / type: protein_or_peptide / ID: 1 / Name.synonym: SOSIP
Details: A SOSIP trimer with the ZM197M isolate sequence with the following mutations: D156N, E295N, V297T and D332N.
Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: ZM197M / synonym: HIV-1
Molecular weightTheoretical: 420 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4

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Macromolecule #2: VRC01 Antibody

MacromoleculeName: VRC01 Antibody / type: protein_or_peptide / ID: 2 / Name.synonym: VRC01
Details: Each Fab consists of a heavy chain-light chain dimer
Number of copies: 3 / Oligomeric state: heterodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 500 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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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

Concentration1.00 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, 150 mM NaCl
GridDetails: 400 mesh carbon support C-flat holey grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER
Method: Added DDM to 0.01% (w/v) to the sample immediately prior to applying sample on grid. Manually blotted and plunged into liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 25500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 180 K / Max: 180 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism was corrected
DateDec 6, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 1914 / Average electron dose: 30.51 e/Å2
Details: Each image is an aligned sum of 32 frames recorded on the K2.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Whole micrograph
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.32 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 4903

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