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- EMDB-25736: HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-25736
TitleHIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab
Map data
Sample
  • Complex: HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab
    • Protein or peptide: HIV Envelope ApexGT3.N130 gp120
    • Protein or peptide: HIV Envelope ApexGT3.N130 gp41
    • Protein or peptide: PG9 Fab Heavy Chain
    • Protein or peptide: PG9 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / germline targeting vaccine / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.75 Å
AuthorsBerndsen ZT / Ward AB
Funding support United States, 4 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1084519 United States
Bill & Melinda Gates FoundationOPP1196345 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 Al100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: Immunity / Year: 2022
Title: Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors.
Authors: Jordan R Willis / Zachary T Berndsen / Krystal M Ma / Jon M Steichen / Torben Schiffner / Elise Landais / Alessia Liguori / Oleksandr Kalyuzhniy / Joel D Allen / Sabyasachi Baboo / ...Authors: Jordan R Willis / Zachary T Berndsen / Krystal M Ma / Jon M Steichen / Torben Schiffner / Elise Landais / Alessia Liguori / Oleksandr Kalyuzhniy / Joel D Allen / Sabyasachi Baboo / Oluwarotimi Omorodion / Jolene K Diedrich / Xiaozhen Hu / Erik Georgeson / Nicole Phelps / Saman Eskandarzadeh / Bettina Groschel / Michael Kubitz / Yumiko Adachi / Tina-Marie Mullin / Nushin B Alavi / Samantha Falcone / Sunny Himansu / Andrea Carfi / Ian A Wilson / John R Yates / James C Paulson / Max Crispin / Andrew B Ward / William R Schief /
Abstract: Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain ...Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain complementarity-determining region 3 (HCDR3), suggesting that the rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy-chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bound inferred germlines for PCT64 and PG9 and had higher affinities for bnAbs, determined cryo-EM structures of ApexGT trimers complexed with inferred-germline and bnAb forms of PCT64 and PG9, and developed an mRNA-encoded cell-surface ApexGT trimer. These methods and immunogens have promise to assist HIV vaccine development.
History
DepositionDec 14, 2021-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25736.png

Downloads & links

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Map

FileDownload / File: emd_25736.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 280 pix.
= 322. Å		1.15 Å/pix.
x 280 pix.
= 322. Å		1.15 Å/pix.
x 280 pix.
= 322. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.749
Minimum - Maximum-1.2645822 - 2.8277674
Average (Standard dev.)0.009916603 (±0.099996224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25736_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25736_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_25736_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab

EntireName: HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab
Components
  • Complex: HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab
    • Protein or peptide: HIV Envelope ApexGT3.N130 gp120
    • Protein or peptide: HIV Envelope ApexGT3.N130 gp41
    • Protein or peptide: PG9 Fab Heavy Chain
    • Protein or peptide: PG9 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab

SupramoleculeName: HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV Envelope ApexGT3.N130 gp120

MacromoleculeName: HIV Envelope ApexGT3.N130 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.477449 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LNCTNVTNNI TDDMRGELKN CSFNATTELR N KRVKRYSL ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LNCTNVTNNI TDDMRGELKN CSFNATTELR N KRVKRYSL FYRLDIVQID SNRTKSHYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NGTGPCPSVS TV QCTHGIK PVVSTQLLLN GSLAEEEVII RSENITNNAK NILVQLNTPV QINCTRPNNN TVKSIRIGPG QAFYYTGDII GDI RQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA QSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWISNTSVQ GSNS TGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRDNWRSE LYKYK VVKI EPLGVAPTRC KRRVVGRRRR RR

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Macromolecule #2: HIV Envelope ApexGT3.N130 gp41

MacromoleculeName: HIV Envelope ApexGT3.N130 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.250541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGTKHHH H HH

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Macromolecule #3: PG9 Fab Heavy Chain

MacromoleculeName: PG9 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.210203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QRLVESGGGV VQPGSSLRLS CAASGFDFSR QGMHWVRQAP GQGLEWVAFI KYDGSEKYHA DSVWGRLSIS RDNSKDTLYL QMNSLRVED TATYFCVREA GGPDYRNGYN (TYS)(TYS)DFYDGYYN YHYMDVWGKG TTVTVSSAST KGPSVFPLAP SSK STSGGT ...String:
QRLVESGGGV VQPGSSLRLS CAASGFDFSR QGMHWVRQAP GQGLEWVAFI KYDGSEKYHA DSVWGRLSIS RDNSKDTLYL QMNSLRVED TATYFCVREA GGPDYRNGYN (TYS)(TYS)DFYDGYYN YHYMDVWGKG TTVTVSSAST KGPSVFPLAP SSK STSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDK KVEPK SCDKGLEVLF Q

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Macromolecule #4: PG9 Fab Light Chain

MacromoleculeName: PG9 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.837256 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCQGTSNDVG GYESVSWYQQ HPGKAPKVVI YDVSKRPSGV SNRFSGSKSG NTASLTISGL QAEDEGDYY CKSLTSTRRR VFGTGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPASV SGSPGQSITI SCQGTSNDVG GYESVSWYQQ HPGKAPKVVI YDVSKRPSGV SNRFSGSKSG NTASLTISGL QAEDEGDYY CKSLTSTRRR VFGTGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHKSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 32 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110183
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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