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- EMDB-21335: Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21335
TitleNanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs
Map dataAMC011FL nanodisc in complex with PGT151 Fab and 10E8 Fab
Sample
  • Complex: Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs
    • Complex: AMC011
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: 10E8 Fab
      • Protein or peptide: Antibody 10E8 Fab heavy chain
      • Protein or peptide: Antibody 10E8 Fab light chain
    • Complex: MPER peptide
      • Protein or peptide: MPER peptide
    • Complex: PGT151 Fab
      • Protein or peptide: Antibody PGT151 Fab heavy chain
      • Protein or peptide: Antibody PGT151 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane / 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
Env polyprotein / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsRantalainen K / Ward ABW
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144462 United States
CitationJournal: Cell Rep / Year: 2020
Title: HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H Zhou / Young D Kwon / William H Law / Chaim A Schramm / Raffaello Verardi / Shelly J Krebs / Peter D Kwong / Nicole A Doria-Rose / Ian A Wilson / Michael B Zwick / John R Yates / William R Schief / Andrew B Ward /
Abstract: Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the ...Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.
History
DepositionFeb 4, 2020-
Header (metadata) releaseMar 4, 2020-
Map releaseApr 22, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.269
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.269
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vpx
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vpx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21335.png

Downloads & links

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Map

FileDownload / File: emd_21335.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC011FL nanodisc in complex with PGT151 Fab and 10E8 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.269 / Movie #1: 0.269
Minimum - Maximum-1.3951252 - 2.1693735
Average (Standard dev.)0.010015027 (±0.06887877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z368.000368.000368.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.3952.1690.010

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Supplemental data

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Mask #1

Fileemd_21335_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AMC011FL nanodisc in complex with PGT151 Fab and 10E8 Fab Half map 1

Fileemd_21335_half_map_1.map
AnnotationAMC011FL nanodisc in complex with PGT151 Fab and 10E8 Fab Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AMC011FL nanodisc in complex with PGT151 Fab and 10E8 Fab Half map 2

Fileemd_21335_half_map_2.map
AnnotationAMC011FL nanodisc in complex with PGT151 Fab and 10E8 Fab Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 ...

EntireName: Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs
Components
  • Complex: Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs
    • Complex: AMC011
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: 10E8 Fab
      • Protein or peptide: Antibody 10E8 Fab heavy chain
      • Protein or peptide: Antibody 10E8 Fab light chain
    • Complex: MPER peptide
      • Protein or peptide: MPER peptide
    • Complex: PGT151 Fab
      • Protein or peptide: Antibody PGT151 Fab heavy chain
      • Protein or peptide: Antibody PGT151 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

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Supramolecule #1: Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 ...

SupramoleculeName: Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: AMC011

SupramoleculeName: AMC011 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: 10E8 Fab

SupramoleculeName: 10E8 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: MPER peptide

SupramoleculeName: MPER peptide / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #5: PGT151 Fab

SupramoleculeName: PGT151 Fab / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.997066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEQLWVTVYY GVPVWKEATT TLFCASDARA YDTEVHNVWA THACVPTDPN PQEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL NCTDLRNSSS GEKMEGGEIK NCSFNITTSM RDKVQKEYAL FYKLDVVPIK NDNTSYRLIS C NTSVITQA ...String:
AEQLWVTVYY GVPVWKEATT TLFCASDARA YDTEVHNVWA THACVPTDPN PQEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL NCTDLRNSSS GEKMEGGEIK NCSFNITTSM RDKVQKEYAL FYKLDVVPIK NDNTSYRLIS C NTSVITQA CPKVSFEPIP IHYCAPAGFA ILKCNDKKFN GTGPCTNVST VQCTHGIRPV VSTQLLLNGS LAEEEVVIRS AN FTDNAKI IIVQLNKSVE INCTRPNNNT RKSIHIGPGR AFYTTGEIIG DIRQAHCNIS GTKWNDTLKQ IVVKLKEQFG NKT IVFNHS SGGDPEIVMH SFNCGGEFFY CNSTQLFNST WNDTEGSNNT KGNGTIVLPC RIKQIVNMWQ EVGKAMYAPP IKGQ IRCSS NITGLILIRD GGNNNESTEI FRPGGGDMRD NWRSELYKYK VVKIEPLGIA PTKAKRRVVQ

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Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.298646 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RLLLSGIVQQ QNNLLRAIEA QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICTTAVPW NTSWSNKSYN QIWNNMTWME WEREIDNYTS LIYTLIEDSQ NQQEKNEQEL LELD

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Macromolecule #3: Antibody 10E8 Fab heavy chain

MacromoleculeName: Antibody 10E8 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.43309 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCSASGFDFD NAWMTWVRQP PGKGLEWVGR ITGPGEGWSV DYAAPVEGRF TISRLNSINF LYLEMNNLR MEDSGLYFCA RTGKYYDFWS GYPPGEEYFQ DWGRGTLVTV

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Macromolecule #4: Antibody 10E8 Fab light chain

MacromoleculeName: Antibody 10E8 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.585818 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
YELTQETGVS VALGRTVTIT CRGDSLRSHY ASWYQKKPGQ APILLFYGKN NRPSGVPDRF SGSASGNRAS LTISGAQAED DAEYYCSSR DKSGSRLSVF GGGTKLTVL

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Macromolecule #5: MPER peptide

MacromoleculeName: MPER peptide / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.147495 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NWFDITNVLW WIKAVIQ

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Macromolecule #6: Antibody PGT151 Fab heavy chain

MacromoleculeName: Antibody PGT151 Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.090016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVESGGGV VQPGKSVRLS CVVSDFPFSK YPMYWVRQAP GKGLEWVAAI SGDAWHVVYS NSVQGRFLVS RDNVKNTLYL EMNSLKIED TAVYRCARMF QESGPPRLDR WSGRNYYYYS GMDVWGQGTT VTVSS

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Macromolecule #7: Antibody PGT151 Fab light chain

MacromoleculeName: Antibody PGT151 Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.94036 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVMTQTPLSL SVTPGQPASI SCKSSESLRQ SNGKTSLYWY RQKPGQSPQL LVFEVSNRFS GVSDRFVGSG SGTDFTLRIS RVEAEDVGF YYCMQSKDFP LTFGGGTKVD

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Macromolecule #17: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 17 / Number of copies: 43 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #18: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

MacromoleculeName: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / type: ligand / ID: 18 / Number of copies: 3 / Formula: 44E
Molecular weightTheoretical: 368.36 Da
Chemical component information

ChemComp-44E:
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / phospholipid*YM

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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

Concentration0.15 mg/mL
BufferpH: 7.4
GridSupport film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsNanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2750 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 128594
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: Ab-initio model generated with cryoSPARC2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.8.0) / Number images used: 40079
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6olp

,

5t80

)
DetailsCoordinates of the fitted models are not refined.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6vpx:
Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs

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