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- EMDB-72009: Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+ -

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Basic information

Entry
Database: EMDB / ID: EMD-72009
TitleQ10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+
Map datasharpened map
Sample
  • Complex: Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+
    • Protein or peptide: Q23 NFL TD CC3+ gp140
    • Protein or peptide: Q10M-055 Fab heavy chain
    • Protein or peptide: Q10M-055 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / macaque / non-human primate / NHP / V2-apex / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPhulera S / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI157299 United States
CitationJournal: Nature / Year: 2026
Title: Vaccination generates broadly cross-neutralizing antibodies to the HIV Env apex.
Authors: Javier Guenaga / Monika Ádori / Shridhar Bale / Swastik Phulera / Ioannis Zygouras / Fabian-Alexander Schleich / Xaquin Castro Dopico / Sashank Agrawal / Miyo Ota / Richard Wilson / Jocelyn ...Authors: Javier Guenaga / Monika Ádori / Shridhar Bale / Swastik Phulera / Ioannis Zygouras / Fabian-Alexander Schleich / Xaquin Castro Dopico / Sashank Agrawal / Miyo Ota / Richard Wilson / Jocelyn Cluff / Tamar Dzvelaia / Marco Mandolesi / Wen-Hsin Lee / Agnes A Walsh / Mariane B Melo / Laurent Verkoczy / Darrell J Irvine / Martin Corcoran / Ian A Wilson / Diane Carnathan / Guido Silvestri / Andrew B Ward / Gabriel Ozorowski / Gunilla B Karlsson Hedestam / Richard T Wyatt /
Abstract: As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly ...As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly neutralizing antibodies, although rare, can be isolated from people living with HIV, revealing conserved envelope glycoprotein (Env) sites as key targets for vaccine development. One such target is the apex of the Env spike. Here we identify a vaccination strategy using heterologous HIV Env trimers covalently coupled to liposomes for multivalent display that resulted in the elicitation of cross-neutralizing HIV serum antibody responses in all trimer-liposome-immunized non-human primates. Critically, we isolated monoclonal antibodies from multiple macaques that cross-neutralize divergent HIV clinical isolates. High-resolution cryogenic electron microscopy structural analyses of monoclonal antibodies from four different macaques demonstrate that they target the Env trimer apex in a manner highly similar to that of the human-infection-elicited, apex-directed broadly neutralizing antibody PG9, representing a substantial advance in HIV vaccine development.
History
DepositionAug 6, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72009.png

Downloads & links

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Map

FileDownload / File: emd_72009.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 400 pix.
= 413.56 Å		1.03 Å/pix.
x 400 pix.
= 413.56 Å		1.03 Å/pix.
x 400 pix.
= 413.56 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0339 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.41535017 - 0.75855005
Average (Standard dev.)0.000040461477 (±0.015986612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 413.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72009_msk_1.map
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Half map: half map B

Fileemd_72009_half_map_1.map
Annotationhalf map B
Projections & Slices
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Histogram

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Half map: half map A

Fileemd_72009_half_map_2.map
Annotationhalf map A
Projections & Slices
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Sample components

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Entire : Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+

EntireName: Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+
Components
  • Complex: Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+
    • Protein or peptide: Q23 NFL TD CC3+ gp140
    • Protein or peptide: Q10M-055 Fab heavy chain
    • Protein or peptide: Q10M-055 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+

SupramoleculeName: Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Q23 NFL TD CC3+ gp140

MacromoleculeName: Q23 NFL TD CC3+ gp140 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 72.431008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VENLWVTVYY GVPVWRDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSAITQAC ...String:
VENLWVTVYY GVPVWRDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSAITQAC PKVSFEPIPI HYCTPAGFAI LKCKDEGFNG TGLCKNVSTV QCTHGIKPVV STQLLLNGSL AEKNITIRSE NI TNNAKII IVQLVQPVTI KCIRPNNYTR KSIRIGPGQA FYAMGDIIGD IRQAHCNVTR SRWNKTLQEV AEKLRTYFGN KTI IFANSS GGDLEITTHS FNCGGEFFYC NTSGLFNSTW YVNSTWNDTD STQESNDTIT LPCRIKQIIN MWQRAGQAMY APPI PGVIK CESNITGLLL TRDGGKDNNV NETFRPGGGD MRDNWRSELY KYKVVEIEPL GVAPTRCKRR VVEGGGGSGG GGSAV GIGA VRRGFLGAAG STMGATSITL TVQARQLLSG IVQPQNNLLR APEAQQHLLK LGVWGIKQLQ ARVLAVERYL RDQQLL GIW GCSGKLICTT NVPWNSSWSN KSLDEIWNNM TWLQWDKEIG NYTQLIYRLI EESQNQQEKN EKELLCLDGG GGSHHHH HH HHGSGC

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Macromolecule #2: Q10M-055 Fab heavy chain

MacromoleculeName: Q10M-055 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 25.175002 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLRLQESGPG LVEPLETLSL TCAVSGGFVS SDYWYWIRQP PGKGLECIGR ISGRHGNTDY SPSLKSRVTI STDTSKNQLS LNLKSVTTA DTAVYYCASD LYYEDD(TYS)GYS YEGLDVFDFW GQGLRVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGC LV KDYFPEPVTV ...String:
QLRLQESGPG LVEPLETLSL TCAVSGGFVS SDYWYWIRQP PGKGLECIGR ISGRHGNTDY SPSLKSRVTI STDTSKNQLS LNLKSVTTA DTAVYYCASD LYYEDD(TYS)GYS YEGLDVFDFW GQGLRVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGC LV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDK

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Macromolecule #3: Q10M-055 Fab light chain

MacromoleculeName: Q10M-055 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.415012 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPAT LSLSPGERAT LSCRASQSVS YNLAWYQQKP GQAPRLLVYG ASSRATGIPD RFSGSGSGTE FTLTITSLEP EDFAFYFCQ QYIHWPTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
EIVMTQSPAT LSLSPGERAT LSCRASQSVS YNLAWYQQKP GQAPRLLVYG ASSRATGIPD RFSGSGSGTE FTLTITSLEP EDFAFYFCQ QYIHWPTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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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

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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

Concentration2.8 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24541
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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