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- EMDB-25376: BG505.MD39TS Env trimer in complex with Fab from antibody C05 -

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Basic information

Entry
Database: EMDB / ID: EMD-25376
TitleBG505.MD39TS Env trimer in complex with Fab from antibody C05
Map dataBG505.MD39TS Env trimer in complex with Fab from antibody C05
Sample
  • Complex: BG505.MD39TS Env trimer in complex with Fab from antibody C05
    • Protein or peptide: Transmembrane protein gp41Transmembrane protein
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: C05 Fab Light chain
    • Protein or peptide: C05 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / identical protein binding / plasma 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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMoore A / Du J / Xu Z / Walker S / Kulp DW / Pallesen J
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 Al109646-04
CitationJournal: Nat Commun / Year: 2022
Title: Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer.
Authors: Ziyang Xu / Susanne Walker / Megan C Wise / Neethu Chokkalingam / Mansi Purwar / Alan Moore / Edgar Tello-Ruiz / Yuanhan Wu / Sonali Majumdar / Kylie M Konrath / Abhijeet Kulkarni / Nicholas ...Authors: Ziyang Xu / Susanne Walker / Megan C Wise / Neethu Chokkalingam / Mansi Purwar / Alan Moore / Edgar Tello-Ruiz / Yuanhan Wu / Sonali Majumdar / Kylie M Konrath / Abhijeet Kulkarni / Nicholas J Tursi / Faraz I Zaidi / Emma L Reuschel / Ishaan Patel / April Obeirne / Jianqiu Du / Katherine Schultheis / Lauren Gites / Trevor Smith / Janess Mendoza / Kate E Broderick / Laurent Humeau / Jesper Pallesen / David B Weiner / Daniel W Kulp /
Abstract: HIV Envelope (Env) is the main vaccine target for induction of neutralizing antibodies. Stabilizing Env into native-like trimer (NLT) conformations is required for recombinant protein immunogens to ...HIV Envelope (Env) is the main vaccine target for induction of neutralizing antibodies. Stabilizing Env into native-like trimer (NLT) conformations is required for recombinant protein immunogens to induce autologous neutralizing antibodies(nAbs) against difficult to neutralize HIV strains (tier-2) in rabbits and non-human primates. Immunizations of mice with NLTs have generally failed to induce tier-2 nAbs. Here, we show that DNA-encoded NLTs fold properly in vivo and induce autologous tier-2 nAbs in mice. DNA-encoded NLTs also uniquely induce both CD4 + and CD8 + T-cell responses as compared to corresponding protein immunizations. Murine neutralizing antibodies are identified with an advanced sequencing technology. The structure of an Env-Ab (C05) complex, as determined by cryo-EM, identifies a previously undescribed neutralizing Env C3/V5 epitope. Beyond potential functional immunity gains, DNA vaccines permit in vivo folding of structured antigens and provide significant cost and speed advantages for enabling rapid evaluation of new HIV vaccines.
History
DepositionNov 4, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25376.png

Downloads & links

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Map

FileDownload / File: emd_25376.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBG505.MD39TS Env trimer in complex with Fab from antibody C05
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.01868737 - 0.045711204
Average (Standard dev.)1.950575e-05 (±0.0011459327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_25376_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_25376_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_25376_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 : BG505.MD39TS Env trimer in complex with Fab from antibody C05

EntireName: BG505.MD39TS Env trimer in complex with Fab from antibody C05
Components
  • Complex: BG505.MD39TS Env trimer in complex with Fab from antibody C05
    • Protein or peptide: Transmembrane protein gp41Transmembrane protein
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: C05 Fab Light chain
    • Protein or peptide: C05 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505.MD39TS Env trimer in complex with Fab from antibody C05

SupramoleculeName: BG505.MD39TS Env trimer in complex with Fab from antibody C05
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 410 KDa

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Macromolecule #1: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.917855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKDAETT LFCASDAKAY ETEKHNVWAT HACVPTDPNP QEIHLENVTE EFNMWKNNMV EQMHEDIISL WDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE Y RLINCNTS ...String:
ENLWVTVYYG VPVWKDAETT LFCASDAKAY ETEKHNVWAT HACVPTDPNP QEIHLENVTE EFNMWKNNMV EQMHEDIISL WDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE Y RLINCNTS AITQACPKVS FEPIPIHYCA PAGFAILKCK DKKFNGTGPC PSVSTVQCTH GIKPVVSTQL LLNGSLAEEE VI IRSENIT NNAKNILVQL NTPVQINCTR PNNNTVKSIR IGPGQAFYYT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKH FGNNTI IRFAQSSGGD LEVTTHSFNC GGEFFYCNTS GLFNSTWISN TSVQGSNSTG SNDSITLPCR IKQIINMWQR IGQA MYAPP IQGVIRCVSN ITGLILTRDG GSTNSTTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TRCKRRV

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Macromolecule #3: C05 Fab Light chain

MacromoleculeName: C05 Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.031465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVLTQSPAS LAVSPGQRAT ISCRPSESVD NYGISFMNWF QQKPGQPPKL LIYAASNRGS GVPARFTGSG SGTDFSLNIH PMEEDDIAM YFCQQSKEVP YTFGGGTKLE IK

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Macromolecule #4: C05 Fab heavy chain

MacromoleculeName: C05 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.727245 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVKLEESGGG LVQAGGSMKL SCVASGFSLS NYWMNWVRQS PEKGLEWVAE IRLKPQNYAT HYAESVKGRF SISRDDSRST VYLQMNNLR AEDTGIYYCT RPGYYGHYAM DYWGQGTSVT VSS

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 41 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration0.05 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 5485 / Average exposure time: 2.59 sec. / Average electron dose: 60.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1455164
Startup modelType of model: EMDB MAP
EMDB ID:

8714

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 121929
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7sq1:
BG505.MD39TS Env trimer in complex with Fab from antibody C05

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