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- EMDB-40088: HIV-1 Env subtype C CZA97.12 SOSIP.664 in complex with 3BNC117 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-40088
TitleHIV-1 Env subtype C CZA97.12 SOSIP.664 in complex with 3BNC117 Fab
Map datasharpened map
Sample
  • Complex: CZA97.12 SOSIP.664 in complex with 3BNC117 Fab
    • Protein or peptide: CZA97.12 SOSIP.664 Envelope glycoprotein gp120
    • Protein or peptide: CZA97.12 SOSIP.664 Envelope glycoprotein gp41
    • Protein or peptide: 3BNC117 Fab heavy chain
    • Protein or peptide: 3BNC117 kappa light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV Envelope / SOSIP / broadly neutralizing antibody / clade C / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 ...: / 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 / 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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsOzorowski G / Lee JH / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: PLoS Pathog / Year: 2023
Title: Glycan heterogeneity as a cause of the persistent fraction in HIV-1 neutralization.
Authors: Rajesh P Ringe / Philippe Colin / Gabriel Ozorowski / Joel D Allen / Anila Yasmeen / Gemma E Seabright / Jeong Hyun Lee / Aleksandar Antanasijevic / Kimmo Rantalainen / Thomas Ketas / John P ...Authors: Rajesh P Ringe / Philippe Colin / Gabriel Ozorowski / Joel D Allen / Anila Yasmeen / Gemma E Seabright / Jeong Hyun Lee / Aleksandar Antanasijevic / Kimmo Rantalainen / Thomas Ketas / John P Moore / Andrew B Ward / Max Crispin / P J Klasse /
Abstract: Neutralizing antibodies (NAbs) to multiple epitopes on the HIV-1-envelope glycoprotein (Env) have been isolated from infected persons. The potency of NAbs is measured more often than the size of the ...Neutralizing antibodies (NAbs) to multiple epitopes on the HIV-1-envelope glycoprotein (Env) have been isolated from infected persons. The potency of NAbs is measured more often than the size of the persistent fraction of infectivity at maximum neutralization, which may also influence preventive efficacy of active or passive immunization and the therapeutic outcome of the latter. Many NAbs neutralize HIV-1 CZA97.012, a clone of a Clade-C isolate, to ~100%. But here NAb PGT151, directed to a fusion-peptide epitope, left a persistent fraction of 15%. NAb PGT145, ligating the Env-trimer apex, left no detectable persistent fraction. The divergence in persistent fractions was further analyzed by depletion of pseudoviral populations of the most PGT151- and PGT145-reactive virions. Thereby, neutralization by the non-depleting NAb increased, whereas neutralization by the depleting NAb decreased. Furthermore, depletion by PGT151 increased sensitivity to autologous neutralization by sera from rabbits immunized with soluble native-like CZA97.012 trimer: substantial persistent fractions were reduced. NAbs in these sera target epitopes comprising residue D411 at the V4-β19 transition in a defect of the glycan shield on CZA97.012 Env. NAb binding to affinity-fractionated soluble native-like CZA97.012 trimer differed commensurately with neutralization in analyses by ELISA and surface plasmon resonance. Glycan differences between PGT151- and PGT145-purified trimer fractions were then demonstrated by mass spectrometry, providing one explanation for the differential antigenicity. These differences were interpreted in relation to a new structure at 3.4-Å resolution of the soluble CZA97.012 trimer determined by cryo-electron microscopy. The trimer adopted a closed conformation, refuting apex opening as the cause of reduced PGT145 binding to the PGT151-purified form. The evidence suggests that differences in binding and neutralization after trimer purification or pseudovirus depletion with PGT145 or PGT151 are caused by variation in glycosylation, and that some glycan variants affect antigenicity through direct effects on antibody contacts, whereas others act allosterically.
History
DepositionMar 15, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40088.png

Downloads & links

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Map

FileDownload / File: emd_40088.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-1.9461192 - 3.9225304
Average (Standard dev.)-0.0013383994 (±0.09627025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 377.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40088_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_40088_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40088_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : CZA97.12 SOSIP.664 in complex with 3BNC117 Fab

EntireName: CZA97.12 SOSIP.664 in complex with 3BNC117 Fab
Components
  • Complex: CZA97.12 SOSIP.664 in complex with 3BNC117 Fab
    • Protein or peptide: CZA97.12 SOSIP.664 Envelope glycoprotein gp120
    • Protein or peptide: CZA97.12 SOSIP.664 Envelope glycoprotein gp41
    • Protein or peptide: 3BNC117 Fab heavy chain
    • Protein or peptide: 3BNC117 kappa light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CZA97.12 SOSIP.664 in complex with 3BNC117 Fab

SupramoleculeName: CZA97.12 SOSIP.664 in complex with 3BNC117 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: CZA97.12 SOSIP.664 Envelope glycoprotein gp120

MacromoleculeName: CZA97.12 SOSIP.664 Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.995121 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARVGNMW VTVYYGVPVW TDAKTTLFCA SDTKAYDREV HNVWATHACV PTDPNPQEI VLENVTENFN MWKNDMVDQM HEDIISLWDQ SLKPCVKLTP LCVTLHCTNA TFKNNVTNDM NKEIRNCSFN T TTEIRDKK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARVGNMW VTVYYGVPVW TDAKTTLFCA SDTKAYDREV HNVWATHACV PTDPNPQEI VLENVTENFN MWKNDMVDQM HEDIISLWDQ SLKPCVKLTP LCVTLHCTNA TFKNNVTNDM NKEIRNCSFN T TTEIRDKK QQGYALFYRP DIVLLKENRN NSNNSEYILI NCNASTITQA CPKVNFDPIP IHYCAPAGYA ILKCNNKTFS GK GPCNNVS TVQCTHGIKP VVSTQLLLNG SLAEKEIIIR SENLTDNVKT IIVHLNKSVE IVCTRPNNNT RKSMRIGPGQ TFY ATGDII GDIRQAYCNI SGSKWNETLK RVKEKLQENY NNNKTIKFAP SSGGDLEITT HSFNCRGEFF YCNTTRLFNN NATE DETIT LPCRIKQIIN MWQGVGRAMY APPIAGNITC KSNITGLLLV RDGGEDNKTE EIFRPGGGNM KDNWRSELYK YKVIE LKPL GIAPTGCKRR VVERRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: CZA97.12 SOSIP.664 Envelope glycoprotein gp41

MacromoleculeName: CZA97.12 SOSIP.664 Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.27967 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RQLLSSIVQQ QSNLLRAPEA QQHMLKLTVW GIKQLQTRVL AIERYLKDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSQT DIWNNMTWME WDREISNYTD TIYRLLEDSQ TQQEKNEKDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 3BNC117 Fab heavy chain

MacromoleculeName: 3BNC117 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.656484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

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Macromolecule #4: 3BNC117 kappa light chain

MacromoleculeName: 3BNC117 kappa light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.022658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS ...String:
DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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: 33 / 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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMsodium chlorideNaClSodium chloride
0.01 % w/vAmphipol A8-35

Details: Detergent added shortly before freezing
GridModel: C-flat-2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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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 / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1142 / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 79261
FSC plot (resolution estimation)

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