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- EMDB-7859: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-7859
TitleFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab
Map dataFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, primary map
Sample
  • Complex: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab
    • Protein or peptide: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151, Light chain
    • Protein or peptide: Immunoglobulin G PCT64_35S Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PCT64_35S, Light chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 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: 0.04
  • 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_7859.png

Downloads & links

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Map

FileDownload / File: emd_7859.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 256 pix.
= 373.76 Å		1.46 Å/pix.
x 256 pix.
= 373.76 Å		1.46 Å/pix.
x 256 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.05317737 - 0.1651219
Average (Standard dev.)-0.0001583287 (±0.0070029404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.461.461.46
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z373.760373.760373.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0530.165-0.000

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Supplemental data

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Half map: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in...

Fileemd_7859_half_map_1.map
AnnotationFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in...

Fileemd_7859_half_map_2.map
AnnotationFull Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S 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 : Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp...

EntireName: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab
Components
  • Complex: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab
    • Protein or peptide: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151, Light chain
    • Protein or peptide: Immunoglobulin G PCT64_35S Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PCT64_35S, Light chain

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Supramolecule #1: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp...

SupramoleculeName: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 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: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043

MacromoleculeName: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVKGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFDMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRNVTGG NLTEEGKEEL KNCSFNATTE LRDKIQKVHS ...String:
MKVKGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFDMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRNVTGG NLTEEGKEEL KNCSFNATTE LRDKIQKVHS LFYRLDLVEL NEGNSSDSNT SMYRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC REKEFNGTGP CKKVSTVQCT HGIKPVVSTQ LLLNGSLAEG KVKIRCENIS NNAKTILVQL TTPVRINCTR PSNNTRTSIR IGPGQSFYAT GDIIGDIRKA YCNVSESEWK EALGKVVEQL RNHFNKTITF ASSSGGDLEI TTHSFNCGGE FFYCNTSSLF NSTWDGNSAT NSTQVPNGTI TLPCRIKQII NMWQRTGQAM YAPPIPGKIR CDSNITGLIL IRDGGNNNNE SETFRPGGGD MRNNWRSELY KYKVVKIDPL GVAPTGAKRR VVEREKRAVG IGAVLFGFLG AAGSTMGAAS LTLTVQARQL LSGIVQQQSN LLRAIEAQQH LLRLTVWGIK QLQARVLAVE RYLSDQQLLG IWGCSGKLIC TTNVPWNSSW SNKSQDEIWN NMTWLQWDKE ISNYTDTIYY LIEKSQNQQE VNEKDLLALD KWTNLWNWFG ISNWLWYIRI FIMIVGGLIG LRIIFAVLSV INRVRQGYSP VSFQTLTPNP RELDRPGGIE EGDGELGKTR SIRLVGGFLA LFWDDLRSLC LFSYHRLRDF ILIAARILEL LGHNSLKGLR LGWEGLKYLG NLLLYWGREL KNSAVNLVDT IAIVVAGWTD RVIEVLQGIG RAFLHIPRRI RQGFERALL

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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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Macromolecule #4: Immunoglobulin G PCT64_35S Fab, Heavy chain

MacromoleculeName: Immunoglobulin G PCT64_35S Fab, Heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL ACVGSEFTFS EAWMTWVRQA PGKGLEWVGH MRPTTEGGAK DYAAAVRGRF TIARDDSKST LYLQMNSLKI EDTGVYYCMT GVERGDFWSD DYSQHYNTYL IDVWGKGTTV TVSS

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Macromolecule #5: Immunoglobulin G PCT64_35S, Light chain

MacromoleculeName: Immunoglobulin G PCT64_35S, Light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGDRAT LSCRATQSVG GDYFAWYQQR PGQSPRLLIY GTSRRAAGIP DRFSGSGSG TDFTLTIDRL EPEDFAVYYC RQYETSFTFG 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER / Details: Specimen was manually frozen.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 980 / Average electron dose: 37.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / 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: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 60093
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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