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- EMDB-7089: HIV-1 Envelope SOSIP trimer clone PC64M4c054 in complex with auto... -

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Basic information

Entry
Database: EMDB / ID: EMD-7089
TitleHIV-1 Envelope SOSIP trimer clone PC64M4c054 in complex with autologous PCT64-13C Fab at 13.2 A resolution
Map dataUnsharpened map from Relion 3D auto-refinement filtered at FSC=0.143 resolution
Sample
  • Complex: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054 in complex with autologous Fab PCT64-13C
    • Protein or peptide: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054
    • Protein or peptide: Immunoglobulin G PCT64-13C Heavy Chain
    • Protein or peptide: Immunoglobulin G PCT64-13C Light Chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.2 Å
AuthorsRantalainen K / Berndsen ZT / Ward AB
CitationJournal: Immunity / Year: 2017
Title: HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.
Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de ...Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de Val / Mengyu Wu / Audrey Cappelletti / Jeffrey Umotoy / Yolanda Lie / Terri Wrin / Paul Algate / Po-Ying Chan-Hui / Etienne Karita / / / Andrew B Ward / Ian A Wilson / Dennis R Burton / Davey Smith / Sergei L Kosakovsky Pond / Pascal Poignard /
Abstract: Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb ...Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design.
History
DepositionOct 24, 2017-
Header (metadata) releaseNov 22, 2017-
Map releaseDec 6, 2017-
UpdateDec 6, 2017-
Current statusDec 6, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00748
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00748
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7089.png

Downloads & links

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Map

FileDownload / File: emd_7089.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map from Relion 3D auto-refinement filtered at FSC=0.143 resolution
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.00748 / Movie #1: 0.00748
Minimum - Maximum-0.0038574429 - 0.024345513
Average (Standard dev.)0.00011015015 (±0.0017716205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0040.0240.000

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Supplemental data

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Mask #1

Fileemd_7089_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map from Relion 3D auto-refinement

Fileemd_7089_half_map_1.map
Annotationunfiltered half map from Relion 3D auto-refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map from Relion 3D auto-refinement

Fileemd_7089_half_map_2.map
Annotationunfiltered half map from Relion 3D auto-refinement
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-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054 in complex...

EntireName: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054 in complex with autologous Fab PCT64-13C
Components
  • Complex: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054 in complex with autologous Fab PCT64-13C
    • Protein or peptide: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054
    • Protein or peptide: Immunoglobulin G PCT64-13C Heavy Chain
    • Protein or peptide: Immunoglobulin G PCT64-13C Light Chain

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Supramolecule #1: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054 in complex...

SupramoleculeName: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054 in complex with autologous Fab PCT64-13C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Fab generated by proteolytic cleavage of IgG antibody
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 275 KDa

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Macromolecule #1: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054

MacromoleculeName: HIV-1 Envelope Glycoprotein SOSIP.664 clone PC64M4c054
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARANNLW VTVYYGVPVW RDAETTLFCA SDAKAYDTEV HNVWATHACV PTDPSPQEIH LANVTEKFNM WKNSMVEQMH TDIISLWDES LKPCVKLTPL CITLNCTNIT RKNVTGGNLT EDGKEELKNC SFNATTELRN ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARANNLW VTVYYGVPVW RDAETTLFCA SDAKAYDTEV HNVWATHACV PTDPSPQEIH LANVTEKFNM WKNSMVEQMH TDIISLWDES LKPCVKLTPL CITLNCTNIT RKNVTGGNLT EDGKEELKNC SFNATTELRN KRQKVHSLFY RLDLVELNEG NSSNSNTSMY RLINCNTSAI TQACPKVSFE PIPIHYCAPA GFAILKCREE EFNGTGPCKN VSTVQCTHGI KPVVSTQLLL NGSLAEGTVK IRCENISNNA KTILVQLTTP VRINCTRPNN NTRTSIRIGP GQSFYATGDI IGDIRKAYCN VSGSEWKEAL GKVVVQLRSH FNKTITFASS SGGDLEITTH SFNCGGEFFY CNTSSLFNST WDGNSTTNST QEPNGTITLP CRIKQIINMW QRTGQAMYAP PIPGKIRCDS NITGLILTRD GENNNTESET FRPEGGDMRN NWRSELYKYK VVKIDPLGVA PTGCKRRVVE RRRRRRAVGI GAVLFGFLGA AGSTMGAASL TLTVQARQLL SGIVQQQSNL LRAPEAQQHL LRLTVWGIKQ LQARVLAVER YLSDQQLLGI WGCSGKLICC TTVPWNSSWS NKSQDEIWNN MTWLQWDKEI SNYTDTIYYL IEKSQNQQEV NEKDLLALD

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Macromolecule #2: Immunoglobulin G PCT64-13C Heavy Chain

MacromoleculeName: Immunoglobulin G PCT64-13C Heavy Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCAASGFTFT NAWLDWVRQA PGKGLEWVGR IKSKTDGGTT DHAAPVKGRF TISRDDSKNT VYLQMNSLKI EDTAVYYCTT GVETYDFWSG YDDHYYDYYF KDVWGKGTTV TVSS

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Macromolecule #3: Immunoglobulin G PCT64-13C Light Chain

MacromoleculeName: Immunoglobulin G PCT64-13C Light Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS NNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQSARSFTFG PGTKVDIK

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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

Concentration5 mg/mL
BufferpH: 7.4
Details: TBS + DDM (added to a final concentration of 0.06 mM prior to vitrification)
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7794 µm / Nominal defocus min: 0.8687 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-43 / Number grids imaged: 1 / Number real images: 100 / Average exposure time: 0.2 sec. / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12343
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 2651

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