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- EMDB-8302: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort... -

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Basic information

Entry
Database: EMDB / ID: EMD-8302
TitleHIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Map dataHIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Sample
  • Complex: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
    • Protein or peptide: PGV04 Fab HC
    • Protein or peptide: PGV04 Fab LC
    • Protein or peptide: AMC011v.4.2_SOSIP
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsPallesen J / de Val N / Ozorowski G / Cottrell CA / Ward AB
CitationJournal: Nat Microbiol / Year: 2016
Title: An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability.
Authors: Marit J van Gils / Tom L G M van den Kerkhof / Gabriel Ozorowski / Christopher A Cottrell / Devin Sok / Matthias Pauthner / Jesper Pallesen / Natalia de Val / Anila Yasmeen / Steven W de ...Authors: Marit J van Gils / Tom L G M van den Kerkhof / Gabriel Ozorowski / Christopher A Cottrell / Devin Sok / Matthias Pauthner / Jesper Pallesen / Natalia de Val / Anila Yasmeen / Steven W de Taeye / Anna Schorcht / Stephanie Gumbs / Inez Johanna / Karen Saye-Francisco / Chi-Hui Liang / Elise Landais / Xiaoyan Nie / Laura K Pritchard / Max Crispin / Garnett Kelsoe / Ian A Wilson / Hanneke Schuitemaker / Per Johan Klasse / John P Moore / Dennis R Burton / Andrew B Ward / Rogier W Sanders /
Abstract: The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals ...The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals develops bNAbs may guide immunization strategies. Here, we describe the isolation and characterization of the bNAb ACS202 from an elite neutralizer that recognizes a new, trimer-specific and cleavage-dependent epitope at the gp120-gp41 interface of the envelope glycoprotein (Env), involving the glycan N88 and the gp41 fusion peptide. In addition, an Env trimer, AMC011 SOSIP.v4.2, based on early virus isolates from the same elite neutralizer, was constructed, and its structure by cryo-electron microscopy at 6.2 Å resolution reveals a closed, pre-fusion conformation similar to that of the BG505 SOSIP.664 trimer. The availability of a native-like Env trimer and a bNAb from the same elite neutralizer provides the opportunity to design vaccination strategies aimed at generating similar bNAbs against a key functional site on HIV-1.
History
DepositionJul 28, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseSep 21, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8302.png

Downloads & links

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Map

FileDownload / File: emd_8302.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.03329188 - 0.081644915
Average (Standard dev.)0.000048965765 (±0.0033451226)
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/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0330.0820.000

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Supplemental data

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Additional map: Additional map: HIV Clade B Env SOSIP ectodomain...

Fileemd_8302_additional.map
AnnotationAdditional map: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map #1: HIV Clade B Env SOSIP...

Fileemd_8302_half_map_1.map
AnnotationHalf map #1: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map #2: HIV Clade B Env SOSIP...

Fileemd_8302_half_map_2.map
AnnotationHalf map #2: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort...

EntireName: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
Components
  • Complex: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
    • Protein or peptide: PGV04 Fab HC
    • Protein or peptide: PGV04 Fab LC
    • Protein or peptide: AMC011v.4.2_SOSIP

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Supramolecule #1: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort...

SupramoleculeName: HIV Clade B Env SOSIP ectodomain trimer from the Amsterdam Cohort Study patient AMC011 in complex with Fab from IgG PGV04
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: PGV04 Fab HC

MacromoleculeName: PGV04 Fab HC / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGSG VKKPGASVRV SCWTSEDIFE RTELIHWVRQ APGQGLEWIG WVKTVTGAVN FGSPDFRQRV SLTRDRDLFT AHMDIRGLTQ GDTATYFCAR QKFYTGGQGW YFDLWGRGTL IVVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA ...String:
QVQLVQSGSG VKKPGASVRV SCWTSEDIFE RTELIHWVRQ APGQGLEWIG WVKTVTGAVN FGSPDFRQRV SLTRDRDLFT AHMDIRGLTQ GDTATYFCAR QKFYTGGQGW YFDLWGRGTL IVVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

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Macromolecule #2: PGV04 Fab LC

MacromoleculeName: PGV04 Fab LC / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGETAS LSCTAASYGH MTWYQKKPGQ PPKLLIFATS KRASGIPDRF SGSQFGKQYT LTITRMEPED FARYYCQQLE FFGQGTRLEI RRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS ...String:
EIVLTQSPGT LSLSPGETAS LSCTAASYGH MTWYQKKPGQ PPKLLIFATS KRASGIPDRF SGSQFGKQYT LTITRMEPED FARYYCQQLE FFGQGTRLEI RRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: AMC011v.4.2_SOSIP

MacromoleculeName: AMC011v.4.2_SOSIP / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEQLW VTVYYGVPVW KEATTTLFCA SDARAYDTEV RNVWATHACV PTDPNPQEVV LENVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTDLR NATNTNATNT TSSSRGTMEG GEIKNCSFNI ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEQLW VTVYYGVPVW KEATTTLFCA SDARAYDTEV RNVWATHACV PTDPNPQEVV LENVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTDLR NATNTNATNT TSSSRGTMEG GEIKNCSFNI TTSMRDKVQK EYALFYKLDV VPIKNDNTSY RLISCNTSVI TQACPKVSFE PIPIHYCAPA GFAILKCNDK KFNGTGPCTN VSTVQCTHGI RPVVSTQLLL NGSLAEEEVV IRSANFTDNA KIIIVQLNKS VEINCTRPNN NTRKSIHIGP GRWFYTTGEI IGDIRQAHCN ISGTKWNDTL KQIVVKLKEQ FGNKTIVFNH SSGGDPEIVM HSFNCGGEFF YCNSTQLFNS TWNDGSNYTG TIVLPCRIKQ IVNMWQEVGK AMYAPPIKGQ IRCSSNITGL ILIRDGGKNR SENTEIFRPG GGDMRDNWRS ELYKYKVVKI EPLGIAPTKC KRRVVQRRRR RRAVGIGAVF LGFLGAAGST MGAASMTLTV QARQLLSGIV QQQNNLLRAP EAQQHLLKLT VWGIKQLQAR VLAVERYLKD QQLLGIWGCS GKLICCTAVP WNTSWSNKSY NQIWNNMTWM EWEREIDNYT SLIYTLIEDS QNQQEKNEQE LLELD

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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

Concentration3.71 mg/mL
BufferpH: 7.4 / Component - Formula: C4H11NO3 / Component - Name: Tris
Details: DDM was added to a concentration of 0.3 mM immediately before freezing.
GridModel: Electron Microscopy Sciences, C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Number real images: 3480 / Average exposure time: 7.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP / Details: EM map of unliganded HIV env trimer
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4b1) / Number images used: 53000
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4b1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4b1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4b1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: MolProbity/RMSD

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