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- EMDB-7863: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-7863
TitleHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
Map dataHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab, primary map
Sample
  • Complex: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664
    • Protein or peptide: Immunoglobulin G PCT64-13C Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PCT64-13C Fab, Light chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsBerndsens ZB / Rantalainen KR / Ward AB
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
History
DepositionMay 9, 2018-
Header (metadata) releaseMay 30, 2018-
Map releaseJun 27, 2018-
UpdateJun 27, 2018-
Current statusJun 27, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7863.png

Downloads & links

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Map

FileDownload / File: emd_7863.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab, primary map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.056611713 - 0.12975307
Average (Standard dev.)0.00026299935 (±0.0055751163)
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
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0570.1300.000

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Supplemental data

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Mask #1

Fileemd_7863_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with...

Fileemd_7863_half_map_1.map
AnnotationHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with...

Fileemd_7863_half_map_2.map
AnnotationHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C 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 : HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex...

EntireName: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
Components
  • Complex: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664
    • Protein or peptide: Immunoglobulin G PCT64-13C Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PCT64-13C Fab, Light chain

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Supramolecule #1: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex...

SupramoleculeName: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64_13C Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664

MacromoleculeName: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664
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 Fab, Heavy chain

MacromoleculeName: Immunoglobulin G PCT64-13C Fab, 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 Fab, Light chain

MacromoleculeName: Immunoglobulin G PCT64-13C Fab, 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

BufferpH: 7.4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400
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: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2006 / Average exposure time: 8.6 sec. / Average electron dose: 81.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 2.0)
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 45661
FSC plot (resolution estimation)

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