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- EMDB-7864: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-7864
TitleHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab
Map dataHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab, primary map
Sample
  • Complex: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A
    • 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 / negative staining / Resolution: 30.0 Å
AuthorsBerndsen ZT / Rantalainen K / 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: 0.0344
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7864.png

Downloads & links

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Map

FileDownload / File: emd_7864.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0344 / Movie #1: 0.0344
Minimum - Maximum-0.060557038 - 0.21514009
Average (Standard dev.)0.00010648611 (±0.008090949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0610.2150.000

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Supplemental data

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Half map: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with...

Fileemd_7864_half_map_1.map
AnnotationHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A 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.N130A in complex with...

Fileemd_7864_half_map_2.map
AnnotationHIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A 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.N130A in c...

EntireName: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab
Components
  • Complex: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A
    • 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.N130A in c...

SupramoleculeName: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #1: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A

MacromoleculeName: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A
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 CITLACTNIT RKNVTGGNLT EDGKEELKNC SFNATTELRN ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARANNLW VTVYYGVPVW RDAETTLFCA SDAKAYDTEV HNVWATHACV PTDPSPQEIH LANVTEKFNM WKNSMVEQMH TDIISLWDES LKPCVKLTPL CITLACTNIT 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

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Nano-W
GridMaterial: COPPER / Pretreatment - Type: PLASMA CLEANING

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 222 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 2395
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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