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- EMDB-9030: HIV-1 Envelope Glycoprotein Clone B41_delCT in complex with the b... -

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Basic information

Entry
Database: EMDB / ID: EMD-9030
TitleHIV-1 Envelope Glycoprotein Clone B41_delCT in complex with the broadly neutralizing antibody Fab PGT151
Map dataprimary map
Sample
  • Complex: HIV-1 Envelope Glycoprotein Clone B41dCT in complex with the broadly neutralizing antibody Fab PGT151
    • Protein or peptide: HIV-1 Envelope Glycoprotein Clone B41_delCT
    • 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: 6.7 Å
AuthorsBerndsen ZT / Ward AB
CitationJournal: Nat Commun / Year: 2018
Title: Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer.
Authors: Liwei Cao / Matthias Pauthner / Raiees Andrabi / Kimmo Rantalainen / Zachary Berndsen / Jolene K Diedrich / Sergey Menis / Devin Sok / Raiza Bastidas / Sung-Kyu Robin Park / Claire M ...Authors: Liwei Cao / Matthias Pauthner / Raiees Andrabi / Kimmo Rantalainen / Zachary Berndsen / Jolene K Diedrich / Sergey Menis / Devin Sok / Raiza Bastidas / Sung-Kyu Robin Park / Claire M Delahunty / Lin He / Javier Guenaga / Richard T Wyatt / William R Schief / Andrew B Ward / John R Yates / Dennis R Burton / James C Paulson /
Abstract: As the sole target of broadly neutralizing antibodies (bnAbs) to HIV, the envelope glycoprotein (Env) trimer is the focus of vaccination strategies designed to elicit protective bnAbs in humans. ...As the sole target of broadly neutralizing antibodies (bnAbs) to HIV, the envelope glycoprotein (Env) trimer is the focus of vaccination strategies designed to elicit protective bnAbs in humans. Because HIV Env is densely glycosylated with 75-90 N-glycans per trimer, most bnAbs use or accommodate them in their binding epitope, making the glycosylation of recombinant Env a key aspect of HIV vaccine design. Upon analysis of three HIV strains, we here find that site-specific glycosylation of Env from infectious virus closely matches Envs from corresponding recombinant membrane-bound trimers. However, viral Envs differ significantly from recombinant soluble, cleaved (SOSIP) Env trimers, strongly impacting antigenicity. These results provide a benchmark for virus Env glycosylation needed for the design of soluble Env trimers as part of an overall HIV vaccine strategy.
History
DepositionAug 8, 2018-
Header (metadata) releaseSep 26, 2018-
Map releaseSep 26, 2018-
UpdateSep 26, 2018-
Current statusSep 26, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0234
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0234
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9030.png

Downloads & links

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Map

FileDownload / File: emd_9030.map.gz / Format: CCP4 / Size: 125 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.)
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: 0.0234 / Movie #1: 0.0234
Minimum - Maximum-0.023851287 - 0.23575324
Average (Standard dev.)0.00040086344 (±0.0048370673)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0240.2360.000

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Supplemental data

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Half map: Half map 1

Fileemd_9030_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_9030_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 B41dCT in complex with the broa...

EntireName: HIV-1 Envelope Glycoprotein Clone B41dCT in complex with the broadly neutralizing antibody Fab PGT151
Components
  • Complex: HIV-1 Envelope Glycoprotein Clone B41dCT in complex with the broadly neutralizing antibody Fab PGT151
    • Protein or peptide: HIV-1 Envelope Glycoprotein Clone B41_delCT
    • 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 B41dCT in complex with the broa...

SupramoleculeName: HIV-1 Envelope Glycoprotein Clone B41dCT in complex with the broadly neutralizing antibody Fab PGT151
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: HIV-1 Envelope Glycoprotein Clone B41_delCT

MacromoleculeName: HIV-1 Envelope Glycoprotein Clone B41_delCT / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTT LFC ASDAKAYDTE VHNVWATHAC VPTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISL WD QSLKPCVKLT PLCVTLNCNN VNTNNTNNST NATISDWEKM ETGEMKNCSF ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTT LFC ASDAKAYDTE VHNVWATHAC VPTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISL WD QSLKPCVKLT PLCVTLNCNN VNTNNTNNST NATISDWEKM ETGEMKNCSF NVTTSIRD K IKKEYALFYK LDVVPLENKN NINNTNITNY RLINCNTSVI TQACPKVSFE PIPIHYCAP AGFAILKCNS KTFNGSGPCT NVSTVQCTHG IRPVVSTQLL LNGSLAEEEI VIRSENITDN AKTIIVQLN EAVEINCTRP NNNTRKSIHI GPGRAFYATG DIIGNIRQAH CNISKARWNE T LGQIVAKL EEQFPNKTII FNHSSGGDPE IVTHSFNCGG EFFYCNTTPL FNSTWNNTRT DD YPTGGEQ NITLQCRIKQ IINMWQGVGK AMYAPPIRGQ IRCSSNITGL LLTRDGGRDQ NGT ETFRPG GGNMRDNWRS ELYKYKVVKI EPLGIAPTAA KRRVVQREKR AVGLGAFILG FLGA AGSTM GAASMALTVQ ARLLLSGIVQ QQNNLLRAIE AQQHMLQLTV WGIKQLQARV LAVER YLRD QQLLGIWGCS GKIICTTNVP WNDSWSNKTI NEIWDNMTWM QWEKEIDNYT QHIYTL LEV SQIQQEKNEQ ELLELDKWDS LWNWFSISNW LWYIKIFIMI VGGLIGLRIV FTVLSII SR VRQGGGSGGG WSHPQFEK

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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
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

Concentration1.13 mg/mL
BufferpH: 7.4
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
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 grids imaged: 1 / Number real images: 2238 / Average exposure time: 8.5 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: MotionCorr2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 6574
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2)
Final 3D classificationSoftware - Name: RELION (ver. 2)
FSC plot (resolution estimation)

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