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- EMDB-45929: LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-45929
TitleLJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
Map datasharpened map
Sample
  • Complex: LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
    • Protein or peptide: JRFL NFL TD CC3+ gp140
    • Protein or peptide: 35O22 heavy chain Fv
    • Protein or peptide: LJF-034 heavy chain Fv
    • Protein or peptide: 35O22 light chain Fv
    • Protein or peptide: LJF-034 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNHP / rhesus macaque / gp120 interface / HIV / NFL / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOzorowski 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: Immunity / Year: 2025
Title: Vaccination of nonhuman primates elicits a broadly neutralizing antibody lineage targeting a quaternary epitope on the HIV-1 Env trimer.
Authors: Fabian-Alexander Schleich / Shridhar Bale / Javier Guenaga / Gabriel Ozorowski / Monika Àdori / Xiaohe Lin / Xaquin Castro Dopico / Richard Wilson / Mark Chernyshev / Alma Teresia Cotgreave ...Authors: Fabian-Alexander Schleich / Shridhar Bale / Javier Guenaga / Gabriel Ozorowski / Monika Àdori / Xiaohe Lin / Xaquin Castro Dopico / Richard Wilson / Mark Chernyshev / Alma Teresia Cotgreave / Marco Mandolesi / Jocelyn Cluff / Esmeralda D Doyle / Leigh M Sewall / Wen-Hsin Lee / Shiyu Zhang / Sijy O'Dell / Brandon S Healy / Deuk Lim / Vanessa R Lewis / Elana Ben-Akiva / Darrell J Irvine / Nicole A Doria-Rose / Martin Corcoran / Diane Carnathan / Guido Silvestri / Ian A Wilson / Andrew B Ward / Gunilla B Karlsson Hedestam / Richard T Wyatt /
Abstract: The elicitation of cross-neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) by vaccination remains a major challenge. Here, we immunized previously Env-immunized nonhuman primates with ...The elicitation of cross-neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) by vaccination remains a major challenge. Here, we immunized previously Env-immunized nonhuman primates with a series of near-native trimers that possessed N-glycan deletions proximal to the conserved CD4 binding site (CD4bs) to focus B cells to this region. Following heterologous boosting with fully glycosylated trimers, we detected tier 2 cross-neutralizing activity in the serum of several animals. Isolation of 185 matched heavy- and light-chain sequences from Env-binding memory B cells from an early responder identified a broadly neutralizing antibody lineage, LJF-0034, which neutralized nearly 70% of an 84-member HIV-1 global panel. High-resolution cryoelectron microscopy (cryo-EM) structures revealed a bifurcated binding mode that bridged the CD4bs to V3 across the gp120:120 interface on two adjacent protomers, evading the proximal N276 glycan impediment to the CD4bs, allowing neutralization breadth. This quaternary epitope defines a potential target for future HIV-1 vaccine development.
History
DepositionJul 25, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45929.png

Downloads & links

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Map

FileDownload / File: emd_45929.map.gz / Format: CCP4 / Size: 343 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.)
1.04 Å/pix.
x 448 pix.
= 463.994 Å		1.04 Å/pix.
x 448 pix.
= 463.994 Å		1.04 Å/pix.
x 448 pix.
= 463.994 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0357 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.53593034 - 0.9188396
Average (Standard dev.)-0.00049302616 (±0.024833284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 463.9936 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45929_msk_1.map
Projections & Slices
AxesZYX

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Half map: half map A

Fileemd_45929_half_map_1.map
Annotationhalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_45929_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 3...

EntireName: LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
Components
  • Complex: LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
    • Protein or peptide: JRFL NFL TD CC3+ gp140
    • Protein or peptide: 35O22 heavy chain Fv
    • Protein or peptide: LJF-034 heavy chain Fv
    • Protein or peptide: 35O22 light chain Fv
    • Protein or peptide: LJF-034 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 3...

SupramoleculeName: LJF-034 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: JRFL NFL TD CC3+ gp140

MacromoleculeName: JRFL 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: 72.573164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VEKLWVTVYY GVPVWKDAET TLFCASDAKA YDTEKHNVWA THACVPTDPN PQEVVLENVT EHFNMWKNNM VEQMQTDIIS LWDQSLKPC VKLTPLCVTL NCKDVNATNT TNDSEGTMER GEIKNCSFNI TTELRDKVQK VYALFYKLDV VPIDNNNTSY R LISCDTSV ...String:
VEKLWVTVYY GVPVWKDAET TLFCASDAKA YDTEKHNVWA THACVPTDPN PQEVVLENVT EHFNMWKNNM VEQMQTDIIS LWDQSLKPC VKLTPLCVTL NCKDVNATNT TNDSEGTMER GEIKNCSFNI TTELRDKVQK VYALFYKLDV VPIDNNNTSY R LISCDTSV ITQACPKISF EPIPIHYCAP AGFAILKCND KTFNGKGPCK NVSTVQCTHG IRPVVSTQLL LNGSLAEEEV VI RSDNFTN NAKTIIVQLK ESVEINCTRP NNYTRKSIRI GPGRAFYTMG EIIGDIRQAH CNISRAKWND TLKQIVIKLR EQF ENKTIV FNHSSGGDPE IVMHSFNCGG EFFYCNSTQL FNSTWNNNTE GSNNTEGNTI TLPCRIKQII NMWQRVGQAM YAPP IRGQI RCSSNITGLL LTRDGGINEN GTEIFRPGGG DMRDNWRSEL YKYKVVKIEP LGVAPTRCKR RVVQGGGGSG GGGSA VGIG AVRRGFLGAA GSTMGAASMT LTVQARNLLS GIVQPQSNLL RAPEAQQRML QLGVWGIKQL QARVLAVERY LRDQQL LGI WGCSGKLICT TAVPWNASWS NKSLDRIWNN MTWMEWEREI DNYTSEIYTL IEESQNQQEK NEQELLCLDG GGGSHHH HH HHHGSGC

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Macromolecule #2: 35O22 heavy chain Fv

MacromoleculeName: 35O22 heavy chain Fv / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.543388 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QGQLVQSGAE LKKPGASVKI SCKTSGYRFN FYHINWIRQT AGRGPEWMGW ISPYSGDKNL APAFQDRVIM TTDTEVPVTS FTSTGAAYM EIRNLKFDDT GTYFCAKGLL RDGSSTWLPY LWGQGTLLTV SS

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Macromolecule #3: LJF-034 heavy chain Fv

MacromoleculeName: LJF-034 heavy chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.612146 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVRPSETLSL ACGVSYGSVD HYYWSWVRQP PGKGLEWIGY IDGYDGATNY SPSLKNRVTI TIDTPNQFSL KMTSVSAAD TAVYFCGRWN LYDDDHAYKS LAVWGRGILV VVSS

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Macromolecule #4: 35O22 light chain Fv

MacromoleculeName: 35O22 light chain Fv / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.400736 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQSASV SGSLGQSVTI SCTGPNSVCC SHKSISWYQW PPGRAPTLII YEDNERAPGI SPRFSGYKSY WSAYLTISDL RPEDETTYY CCSYTHNSGC VFGTGTKVSV LGQSK

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Macromolecule #5: LJF-034 light chain Fv

MacromoleculeName: LJF-034 light chain Fv / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.737059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDTVT ITCRARHGVG ENLNWYQQKP GKAPKVLIYM ASSRQSGIPS RFRGGGSGTE FTLTISSLQP EDFGTYHCQ QSYSYPWTFG QGTKVEIK

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 34 / 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

Concentration7.8 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris pH 7.4, 150 mM NaCl, 0.06 mM DDM
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
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: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49048
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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