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- EMDB-23518: Cryo-EM map of DH851.3 bound to HIV-1 CH505 Env -

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Entry
Database: EMDB / ID: EMD-23518
TitleCryo-EM map of DH851.3 bound to HIV-1 CH505 Env
Map dataCryoEM map of DH851.3 bound to HIV-1 CH505 Env
Sample
  • Complex: DH851.3 bound to HIV-1 CH505 Env
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFab-dimerized / glycan-reactive / antibodies / HIV-1 / DH898.1 / Fab-dimer / glycan-reactive neutralizing antibody / macaque HIV-1 vaccine-induced / B cell lineage / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsEdwards RJ / Manne K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)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: Acharya P / Williams W / Henderson R / Janowska K / Manne K / Parks R / Deyton M / Sprenz J / Stalls V / Kopp M / Mansouri K / Edwards RJ / Meyerhoff RR / Oguin T / Sempowski G / Saunders K / Haynes BF
History
DepositionFeb 21, 2021-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lu9
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23518.png

Downloads & links

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Map

FileDownload / File: emd_23518.map.gz / Format: CCP4 / Size: 27.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of DH851.3 bound to HIV-1 CH505 Env
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 141 pix.
= 150.376 Å		1.07 Å/pix.
x 223 pix.
= 237.829 Å		1.07 Å/pix.
x 232 pix.
= 247.428 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.0665 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.4758269 - 0.89355016
Average (Standard dev.)0.000000000000366 (±0.040937867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin9875121
Dimensions223232141
Spacing141223232
CellA: 150.3765 Å / B: 237.82948 Å / C: 247.428 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06649645390071.06649775784751.0665
M x/y/z141223232
origin x/y/z0.0000.0000.000
length x/y/z150.376237.829247.428
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S321
start NC/NR/NS7598121
NC/NR/NS232223141
D min/max/mean-0.4760.8940.000

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Supplemental data

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Half map: CryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env

Fileemd_23518_half_map_1.map
AnnotationCryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env

Fileemd_23518_half_map_2.map
AnnotationCryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DH851.3 bound to HIV-1 CH505 Env

EntireName: DH851.3 bound to HIV-1 CH505 Env
Components
  • Complex: DH851.3 bound to HIV-1 CH505 Env
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: DH851.3 bound to HIV-1 CH505 Env

SupramoleculeName: DH851.3 bound to HIV-1 CH505 Env / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: DH851.3 light chain

MacromoleculeName: DH851.3 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.127463 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN ...String:
ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN NKYAASSYLS LTSDQWKSHK SYSCQVTHEG STVEKTVAPA EC

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Macromolecule #2: DH851.3 heavy chain

MacromoleculeName: DH851.3 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.451617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String:
QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTCGG

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Macromolecule #3: DH851.3 heavy chain

MacromoleculeName: DH851.3 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.89093 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String:
QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVE

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Macromolecule #4: DH851.3 light chain

MacromoleculeName: DH851.3 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 21.824127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN ...String:
ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN NKYAASSYLS LTSDQWKSHK SYSCQVTHEG STVEKTVAP

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Macromolecule #5: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134512 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLKAIEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #6: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.898062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV ...String:
ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV SFDPIPIHYC APAGYAILKC NNKTFTGTGP CNNVSTVQCT HGIKPVVSTQ LLLNGSLAEG EIIIRSENIT NN VKTIIVH LNESVKIECT RPNNKTRTSI RIGPGQWFYA TGQVIGDIRE AYCNINESKW NETLQRVSKK LKEYFPHKNI TFQ PSSGGD LEITTHSFNC GGEFFYCNTS SLFNRTYMAN STDMANSTET NSTRTITIHC RIKQIINMWQ EVGRAMYAPP IAGN ITCIS NITGLLLTRD GGKNNTETFR PGGGNMKDNW RSELYKYKVV KIEPLGVAPT RCKRRV

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: blot for 2.5 seconds before plunging.

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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 grids imaged: 6058 / 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
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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53398
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7lu9:
Cryo-EM structure of DH851.3 bound to HIV-1 CH505 Env

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