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- EMDB-7107: HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-7107
TitleHIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP in complex with PGV04 Fab
Map dataprimary map
Sample
  • Complex: HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP.664 in complex with PGV04 Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP.664
    • Protein or peptide: Human IgG Fab PGV04 Heavy Chain
    • Protein or peptide: Human IgG Fab PGV04 Heavy Chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsBerndsen ZT / Rantalainen K / 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
DepositionNov 7, 2017-
Header (metadata) releaseDec 6, 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: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7107.png

Downloads & links

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Map

FileDownload / File: emd_7107.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 64 pix.
= 262.4 Å		4.1 Å/pix.
x 64 pix.
= 262.4 Å		4.1 Å/pix.
x 64 pix.
= 262.4 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: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.045905747 - 0.17662056
Average (Standard dev.)0.0010671521 (±0.017476585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0460.1770.001

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Supplemental data

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Half map: half map 1

Fileemd_7107_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_7107_half_map_2.map
Annotationhalf 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 PGV04 Fab
Components
  • Complex: HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP.664 in complex with PGV04 Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein clone PC64M4c054 SOSIP.664
    • Protein or peptide: Human IgG Fab PGV04 Heavy Chain
    • Protein or peptide: Human IgG Fab PGV04 Heavy 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 PGV04 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 225 KDa

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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 RRGAR ANNL WVTVYYGVPV WRDAETTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQEI HLANVTEKFN MWKNSMVEQM HTDIISLWDE SLKPCVKLTP LCITLNCTNI TRKNVTGGNL TEDGKEELKN CSFNATTELR ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGAR ANNL WVTVYYGVPV WRDAETTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQEI HLANVTEKFN MWKNSMVEQM HTDIISLWDE SLKPCVKLTP LCITLNCTNI TRKNVTGGNL TEDGKEELKN CSFNATTELR NKRQKVHSLF YRLDLVELNE GNSSNSNTSM YRLINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCRE EEFNGTGPCK NVSTVQCTHG IKPVVSTQLL LNGSLAEGTV KIRCENISNN AKTILVQLTT PVRINCTRPN NNTRTSIRIG PGQSFYATGD IIGDIRKAYC NVSGSEWKEA LGKVVVQLRS HFNKTITFAS SSGGDLEITT HSFNCGGEFF YCNTSSLFNS TWDGNSTTNS TQEPNGTITL PCRIKQIINM WQRTGQAMYA PPIPGKIRCD SNITGLILTR DGENNNTESE TFRPEGGDMR NNWRSELYKY KVVKIDPLGV APTGCKRRVV ERRRRRRAVG IGAVLFGFLG AAGSTMGAAS LTLTVQARQL LSGIVQQQSN LLRAPEAQQH LLRLTVWGIK QLQARVLAVE RYLSDQQLLG IWGCSGKLIC CTTVPWNSSW SNKSQDEIWN NMTWLQWDKE ISNYTDTIYY LIEKSQNQQE VNEKDLLALD

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Macromolecule #2: Human IgG Fab PGV04 Heavy Chain

MacromoleculeName: Human IgG Fab PGV04 Heavy Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: qvqlvqsgsg vkkpgasvr v scwtsedi fe rtelihw vrq apgqgl ewig wvktv tgavn fgsp dfrqrv slt rdrdlft ah mdirgltq g dtatyfcar qkfytggqgw yfdlwgrgt l ivvssast kg psvfpla pss kstsgg taal gclvk ...String:
qvqlvqsgsg vkkpgasvr v scwtsedi fe rtelihw vrq apgqgl ewig wvktv tgavn fgsp dfrqrv slt rdrdlft ah mdirgltq g dtatyfcar qkfytggqgw yfdlwgrgt l ivvssast kg psvfpla pss kstsgg taal gclvk dyfpe pvtv swnsga lts gvhtfpa vl qssglysl s svvtvpsss lgtqtyicnv nhkpsntkv d kkvepksc

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Macromolecule #3: Human IgG Fab PGV04 Heavy Chain

MacromoleculeName: Human IgG Fab PGV04 Heavy Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: eivltqspgt lslspgeta s lsctaasy gh mtwyqkk pgq ppklli fats krasg ipdrf sgsq fgkqyt lti trmeped fa ryycqqle f fgqgtrlei rrtvaapsvf ifppsdeql k sgtasvvc ll nnfypre akv qwkvdn alqs gnsqe ...String:
eivltqspgt lslspgeta s lsctaasy gh mtwyqkk pgq ppklli fats krasg ipdrf sgsq fgkqyt lti trmeped fa ryycqqle f fgqgtrlei rrtvaapsvf ifppsdeql k sgtasvvc ll nnfypre akv qwkvdn alqs gnsqe svteq dskd stysls stl tlskady ek hkvyacev t hqglsspvt ksfnrgec

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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: NanoW
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average exposure time: 0.5 sec. / 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

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 11429
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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