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- EMDB-8181: Broadly neutralizing antibody PGDM14 in complex with BG505 SOSIP.... -

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Basic information

Entry
Database: EMDB / ID: EMD-8181
TitleBroadly neutralizing antibody PGDM14 in complex with BG505 SOSIP.664 Env trimer
Map dataBroadly neutralizing antibody PGDM14 in complex with BG505 SOSIP.664 Env trimer
Sample
  • Complex: BG505 SOSIP.664 trimer in complex with PGDM14 Fab
    • Protein or peptide: BG505 SOSIP.664 soluble Env trimer
    • Protein or peptide: Heavy chain Fab of broadly neutralizing antibody PGDM14
    • Protein or peptide: Light chain of broadly neutralizing antibody PGDM14
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsLee JH / Ward AB
CitationJournal: Immunity / Year: 2016
Title: A Prominent Site of Antibody Vulnerability on HIV Envelope Incorporates a Motif Associated with CCR5 Binding and Its Camouflaging Glycans.
Authors: Devin Sok / Matthias Pauthner / Bryan Briney / Jeong Hyun Lee / Karen L Saye-Francisco / Jessica Hsueh / Alejandra Ramos / Khoa M Le / Meaghan Jones / Joseph G Jardine / Raiza Bastidas / ...Authors: Devin Sok / Matthias Pauthner / Bryan Briney / Jeong Hyun Lee / Karen L Saye-Francisco / Jessica Hsueh / Alejandra Ramos / Khoa M Le / Meaghan Jones / Joseph G Jardine / Raiza Bastidas / Anita Sarkar / Chi-Hui Liang / Sachin S Shivatare / Chung-Yi Wu / William R Schief / Chi-Huey Wong / Ian A Wilson / Andrew B Ward / Jiang Zhu / Pascal Poignard / Dennis R Burton /
Abstract: The dense patch of high-mannose-type glycans surrounding the N332 glycan on the HIV envelope glycoprotein (Env) is targeted by multiple broadly neutralizing antibodies (bnAbs). This region is ...The dense patch of high-mannose-type glycans surrounding the N332 glycan on the HIV envelope glycoprotein (Env) is targeted by multiple broadly neutralizing antibodies (bnAbs). This region is relatively conserved, implying functional importance, the origins of which are not well understood. Here we describe the isolation of new bnAbs targeting this region. Examination of these and previously described antibodies to Env revealed that four different bnAb families targeted the (324)GDIR(327) peptide stretch at the base of the gp120 V3 loop and its nearby glycans. We found that this peptide stretch constitutes part of the CCR5 co-receptor binding site, with the high-mannose patch glycans serving to camouflage it from most antibodies. GDIR-glycan bnAbs, in contrast, bound both (324)GDIR(327) peptide residues and high-mannose patch glycans, which enabled broad reactivity against diverse HIV isolates. Thus, as for the CD4 binding site, bnAb effectiveness relies on circumventing the defenses of a critical functional region on Env.
History
DepositionMay 13, 2016-
Header (metadata) releaseJul 20, 2016-
Map releaseAug 3, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8181.png

Downloads & links

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Map

FileDownload / File: emd_8181.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBroadly neutralizing antibody PGDM14 in complex with BG505 SOSIP.664 Env trimer
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.01809887 - 0.055732537
Average (Standard dev.)0.00032249984 (±0.0048149377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0180.0560.000

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Supplemental data

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Sample components

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Entire : BG505 SOSIP.664 trimer in complex with PGDM14 Fab

EntireName: BG505 SOSIP.664 trimer in complex with PGDM14 Fab
Components
  • Complex: BG505 SOSIP.664 trimer in complex with PGDM14 Fab
    • Protein or peptide: BG505 SOSIP.664 soluble Env trimer
    • Protein or peptide: Heavy chain Fab of broadly neutralizing antibody PGDM14
    • Protein or peptide: Light chain of broadly neutralizing antibody PGDM14

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Supramolecule #1: BG505 SOSIP.664 trimer in complex with PGDM14 Fab

SupramoleculeName: BG505 SOSIP.664 trimer in complex with PGDM14 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4

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Macromolecule #1: BG505 SOSIP.664 soluble Env trimer

MacromoleculeName: BG505 SOSIP.664 soluble Env trimer / type: protein_or_peptide / ID: 1
Details: This soluble Env sequence is derived from HIV-1 isolate BG505. It contains mutations to generate the N332 N-linked glycosylation site (T332N) and has stabilizing mutations A501C, I559P, and ...Details: This soluble Env sequence is derived from HIV-1 isolate BG505. It contains mutations to generate the N332 N-linked glycosylation site (T332N) and has stabilizing mutations A501C, I559P, and T605C. The construct is truncated at residue 664 of GP41.
Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MIRSENITNN AKNILVQFNT PVQINCTRPN NNTRKSIRIG PGQAFYATGD IIGDIRQAHC NVSKATWNET LGKVVKQLRK HFGNNTIIRF ANSSGGDLEV TTHSFNCGGE FFYCNTSGLF NSTWISNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGRRRRR RAVGIGAVFL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQSNLLRAPE AQQHLLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #2: Heavy chain Fab of broadly neutralizing antibody PGDM14

MacromoleculeName: Heavy chain Fab of broadly neutralizing antibody PGDM14
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCTASGYYMS WIRQAPGKGL EWIAYISLRN NGYTHYADSV KGRFTMSRDY AKNLMFLQMN SLRVDDTAIY YCARVASGPN EDFYHDTEAA FDIWGQGTPV FVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL ...String:
EVQLVESGGG LVKPGGSLRL SCTASGYYMS WIRQAPGKGL EWIAYISLRN NGYTHYADSV KGRFTMSRDY AKNLMFLQMN SLRVDDTAIY YCARVASGPN EDFYHDTEAA FDIWGQGTPV FVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCD

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Macromolecule #3: Light chain of broadly neutralizing antibody PGDM14

MacromoleculeName: Light chain of broadly neutralizing antibody PGDM14 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTTLS SPVTLGQAAS ISCKSSRNLV NSDGNTYLSW LHQR PGQPP SLLIYKISRR FSGVSDRFSG SGAGTDFTLR INRVEAADVG VYYCMQGSHW AWA FGQGTK LHVNRRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES ...String:
DIVMTQTTLS SPVTLGQAAS ISCKSSRNLV NSDGNTYLSW LHQR PGQPP SLLIYKISRR FSGVSDRFSG SGAGTDFTLR INRVEAADVG VYYCMQGSHW AWA FGQGTK LHVNRRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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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

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloridesodium chloride
StainingType: NEGATIVE / Material: 2% uranyl formate
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
TemperatureMax: 298.0 K
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 2 / Number real images: 223 / Average electron dose: 25.0 e/Å2

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Image processing

Startup modelType of model: OTHER
Details: Common lines model generated from reference-free 2D class averages
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPARX / Software - details: sxali3d.py
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Software - details: sxali3d.py / Number images used: 8493

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