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- EMDB-23124: Cryo-electron microcospy reconstruction of CH848.3.D0949.10.17chi... -

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Entry
Database: EMDB / ID: EMD-23124
TitleCryo-electron microcospy reconstruction of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Map dataFinal sharpened map of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Sample
  • Complex: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer in the presence of but not bound to DH898.1 Fab
    • Protein or peptide: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120
    • Protein or peptide: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsEdwards RJ / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI140897 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
Citation
Journal: Cell / Year: 2021
Title: Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.
Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler ...Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler Evangelous / Bhavna Hora / Madison Berry / A Yousef Abuahmad / Jordan Sprenz / Margaret Deyton / Victoria Stalls / Megan Kopp / Allen L Hsu / Mario J Borgnia / Guillaume B E Stewart-Jones / Matthew S Lee / Naomi Bronkema / M Anthony Moody / Kevin Wiehe / Todd Bradley / S Munir Alam / Robert J Parks / Andrew Foulger / Thomas Oguin / Gregory D Sempowski / Mattia Bonsignori / Celia C LaBranche / David C Montefiori / Michael Seaman / Sampa Santra / John Perfect / Joseph R Francica / Geoffrey M Lynn / Baptiste Aussedat / William E Walkowicz / Richard Laga / Garnett Kelsoe / Kevin O Saunders / Daniela Fera / Peter D Kwong / Robert A Seder / Alberto Bartesaghi / George M Shaw / Priyamvada Acharya / Barton F Haynes /
Abstract: Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) ...Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgMIgDCD27, thus suggesting that they originated from a pool of antigen-experienced IgM or marginal zone B cells.
#1: Journal: bioRxiv / Year: 2020
Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N ...Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N / Perfect J / Moody MA / Wiehe K / Bradley T / Kepler TB / Alam SM / Foulger A / Bonsignori M / LaBranche CC / Montefiori DC / Seaman M / Santra S / Francica JR / Lynn GM / Aussedat B / Walkowicz WE / Laga R / Kelso G / Saunders KO / Fera D / Kwong PD / Seder RA / Bartesaghi A / Shaw GM / Acharya P / Haynes BF
History
DepositionDec 16, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l6o
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23124.png

Downloads & links

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Map

FileDownload / File: emd_23124.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpened map of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.023 Å		1.07 Å/pix.
x 256 pix.
= 273.023 Å		1.07 Å/pix.
x 256 pix.
= 273.023 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0665 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-0.5204865 - 1.6141689
Average (Standard dev.)0.0125683425 (±0.06454605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.02298 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.066496093751.066496093751.06649609375
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.023273.023273.023
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5201.6140.013

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Supplemental data

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Mask #1

Fileemd_23124_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_23124_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env

Fileemd_23124_additional_1.map
AnnotationUnsharpened map of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution of of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env...

Fileemd_23124_additional_2.map
AnnotationLocal resolution of of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env

Fileemd_23124_half_map_1.map
AnnotationHalf-map A of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half-map B of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env

Fileemd_23124_half_map_2.map
AnnotationHalf-map B of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer...

EntireName: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer in the presence of but not bound to DH898.1 Fab
Components
  • Complex: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer in the presence of but not bound to DH898.1 Fab
    • Protein or peptide: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120
    • Protein or peptide: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41

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Supramolecule #1: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer...

SupramoleculeName: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer in the presence of but not bound to DH898.1 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: CH848 10.17
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F
Molecular weightTheoretical: 209.7 KDa

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Macromolecule #1: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120

MacromoleculeName: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSNATVKNG TVEEMKNCSF NTTTEIRDKE KKEYALFYKP DIVPLSETNN TSEYRLINCN T SACTQACP ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSNATVKNG TVEEMKNCSF NTTTEIRDKE KKEYALFYKP DIVPLSETNN TSEYRLINCN T SACTQACP KVTFEPIPIH YCAPAGYAIL KCNDETFNGT GPCSNVSTVQ CTHGIRPVVS TQLLLNGSLA EKEIVIRSEN LT NNAKIII VHLHTPVEIV CTRPNNNTRK SVRIGPGQTF YATGDIIGDI KQAHCNISEE KWNDTLQKVG IELQKHFPNK TIK YNQSAG GDMEITTHSF NCGGEFFYCN TSNLFNGTYN GTYISTNSSA NSTSTITLQC RIKQIINMWQ GVGRCMYAPP IAGN ITCRS NITGLLLTRD GGTNSNETET FRPAGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG R

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Macromolecule #2: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41

MacromoleculeName: CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString:
FLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PEAQQHLLKL TVWGIKQLQA RVLAVERYLR DQQLLGIWGC SGKLICCTN VPWNSSWSNR NLSEIWDNMT WLQWDKEISN YTQIIYGLLE ESQNQQEKNE QDLLALD

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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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
5.0 mMHEPES buffer
150.0 mMsodium chlorideNaCl
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Pressure: 0.039 kPa / Details: Glow discharged for 30 s in PELCO easiGlow(TM).
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
Details: 2.5 microliter of smaple applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.15 K / Max: 93.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3230 / Average exposure time: 4.0 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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1655400
Details: Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were ...Details: Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were extracted with a 320-pixel box size and subjected to 2D class averaging with 100 classes. From these, seven classes were chosen for template picking applied to the full final micrograph set, yielding 1,655,400 particles
CTF correctionSoftware - Name: cryoSPARC
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6um6

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 48127
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 17329 / Software - Name: cryoSPARC (ver. 2.15.0) / Details: Ab initio
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6um6

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7l6o:
Cryo-EM structure of HIV-1 Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664

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