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- EMDB-25735: HIV-1 Envelope ApexGT3 in complex with PG9.iGL Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-25735
TitleHIV-1 Envelope ApexGT3 in complex with PG9.iGL Fab
Map data
Sample
  • Complex: HIV-1 Envelope ApexGT3 in complex with PG9.iGL Fab
    • Protein or peptide: HIV Envelope ApexGT3 gp120
    • Protein or peptide: HIV Envelope ApexGT3 gp41
    • Protein or peptide: PG9.iGL Fab Light Chain
    • Protein or peptide: PG9.iGL Fab Heavy 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: 4.43 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-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25735.png

Downloads & links

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Map

FileDownload / File: emd_25735.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.638
Minimum - Maximum-1.4688964 - 2.7195597
Average (Standard dev.)0.0025368463 (±0.09311225)
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_25735_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25735_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_25735_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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

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

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

SupramoleculeName: HIV-1 Envelope ApexGT3 in complex with PG9.iGL 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 gp120

MacromoleculeName: HIV Envelope ApexGT3 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.461449 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNATTELR N KRVKRYSL ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNATTELR N KRVKRYSL FYRLDIVQID SNRAKSHYRL 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 gp41

MacromoleculeName: HIV Envelope ApexGT3 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.iGL Fab Light Chain

MacromoleculeName: PG9.iGL Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.139408 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLNSTSLFRF LFCAVTDPSC DRRLPEINMY RMQLLSCIAL SLALVTNSQS ALTQPASVSG SPGQSITISC TGTSSDVGGY NYVSWYQQH PGKAPKLMIY EVSNRPSGVS NRFSGSKSGN TASLTISGLQ AEDEADYYCS SYTSSSTVVF GGGTKLTVLG Q PKAAPSVT ...String:
MLNSTSLFRF LFCAVTDPSC DRRLPEINMY RMQLLSCIAL SLALVTNSQS ALTQPASVSG SPGQSITISC TGTSSDVGGY NYVSWYQQH PGKAPKLMIY EVSNRPSGVS NRFSGSKSGN TASLTISGLQ AEDEADYYCS SYTSSSTVVF GGGTKLTVLG Q PKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLSLTPEQWK SH RSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #4: PG9.iGL Fab Heavy Chain

MacromoleculeName: PG9.iGL Fab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.41884 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGMHWVRQA PGKGLEWVAV ISYDGSNKYY ADSVKGRFT ISRDNSKNTL YLQMNSLRAE DTAVYYCARE AGGPDYRNG(TYS) NY(TYS)DFWSGYY YYYYMDVWGK GTT VTVSSA ...String:
MYRMQLLSCI ALSLALVTNS QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGMHWVRQA PGKGLEWVAV ISYDGSNKYY ADSVKGRFT ISRDNSKNTL YLQMNSLRAE DTAVYYCARE AGGPDYRNG(TYS) NY(TYS)DFWSGYY YYYYMDVWGK GTT VTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSS LGTQT YICNVNHKPS NTKVDKKVEP KSC

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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: 28 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78573
FSC plot (resolution estimation)

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