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- EMDB-7860: HIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664 complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-7860
TitleHIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664 complex with PGT151 Fab
Map dataHIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664 complex with PGT151 Fab, full map
Sample
  • Complex: HIV-1 Envelope glycoprotein clone PC64M18C043.SOSIP.664 in complex with PGT151 Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151, Light chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7860.png

Downloads & links

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Map

FileDownload / File: emd_7860.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664 complex with PGT151 Fab, full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.042855073 - 0.1245059
Average (Standard dev.)0.00030930634 (±0.0053250967)
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-0.0430.1250.000

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Supplemental data

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Mask #1

Fileemd_7860_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 PC64M18C043.SOSIP.664 complex with PGT151...

Fileemd_7860_half_map_1.map
AnnotationHIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664 complex with PGT151 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 PC64M18C043.SOSIP.664 complex with PGT151...

Fileemd_7860_half_map_2.map
AnnotationHIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664 complex with PGT151 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 PC64M18C043.SOSIP.664 in comple...

EntireName: HIV-1 Envelope glycoprotein clone PC64M18C043.SOSIP.664 in complex with PGT151 Fab
Components
  • Complex: HIV-1 Envelope glycoprotein clone PC64M18C043.SOSIP.664 in complex with PGT151 Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M18C043.SOSIP.664
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151, Light chain

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Supramolecule #1: HIV-1 Envelope glycoprotein clone PC64M18C043.SOSIP.664 in comple...

SupramoleculeName: HIV-1 Envelope glycoprotein clone PC64M18C043.SOSIP.664 in complex with PGT151 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 PC64M18C043.SOSIP.664

MacromoleculeName: HIV-1 Envelope Glycoprotein clone PC64M18C043.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 RRGARAANNL WVTVYYGVPV WRDAETTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQEI HLANVTEKFD MWKNSMVEQM HTDIISLWDE SLKPCVKLTP LCITLNCTNI TRNVTGGNLT EEGKEELKNC SFNATTELRD ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAANNL WVTVYYGVPV WRDAETTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQEI HLANVTEKFD MWKNSMVEQM HTDIISLWDE SLKPCVKLTP LCITLNCTNI TRNVTGGNLT EEGKEELKNC SFNATTELRD KIQKVHSLFY RLDLVELNEG NSSDSNTSMY RLINCNTSAI TQACPKVSFE PIPIHYCAPA GFAILKCREK EFNGTGPCKK VSTVQCTHGI KPVVSTQLLL NGSLAEGKVK IRCENISNNA KTILVQLTTP VRINCTRPSN NTRTSIRIGP GQSFYATGDI IGDIRKAYCN VSESEWKEAL GKVVEQLRNH FNKTITFASS SGGDLEITTH SFNCGGEFFY CNTSSLFNST WDGNSATNST QVPNGTITLP CRIKQIINMW QRTGQAMYAP PIPGKIRCDS NITGLILIRD GGNNNNESET FRPGGGDMRN NWRSELYKYK VVKIDPLGVA PTGCKRRVVE RRRRRRAVGI GAVLFGFLGA AGSTMGAASL TLTVQARQLL SGIVQQQSNL LRAPEAQQHL LRLTVWGIKQ LQARVLAVER YLSDQQLLGI WGCSGKLICC TNVPWNSSWS NKSQDEIWNN MTWLQWDKEI SNYTDTIYYL IEKSQNQQEV NEKDLLALD

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Macromolecule #2: Immunoglobulin G PGT151 Fab, Heavy chain

MacromoleculeName: Immunoglobulin G PGT151 Fab, Heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF ...String:
RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DK

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Macromolecule #3: Immunoglobulin G PGT151, Light chain

MacromoleculeName: Immunoglobulin G PGT151, Light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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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

Concentration7 mg/mL
BufferpH: 7.4
Details: Detergent removed with Biobeads prior to grid freezing
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1555 / Average electron dose: 81.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Startup modelType of model: EMDB MAP
EMDB ID:

3309

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 34864
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
FSC plot (resolution estimation)

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