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- EMDB-45928: LJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-45928
TitleLJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
Map datasharpened map
Sample
  • Complex: LJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
    • Protein or peptide: 35O22 heavy chain Fv
    • Protein or peptide: 35O22 light chain Fv
    • Protein or peptide: LJF-085 heavy chain Fv
    • Protein or peptide: LJF-085 light chain Fv
    • Protein or peptide: HIV Env JRFL NFL TD CC3+ gp140
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNHP / rhesus macaque / gp120 interface / HIV / NFL / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / identical protein binding / 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) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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_45928.png

Downloads & links

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Map

FileDownload / File: emd_45928.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.)
1.03 Å/pix.
x 448 pix.
= 459.514 Å		1.03 Å/pix.
x 448 pix.
= 459.514 Å		1.03 Å/pix.
x 448 pix.
= 459.514 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0257 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.46914136 - 0.78613734
Average (Standard dev.)-0.00048393934 (±0.01966042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 459.51358 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45928_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_45928_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_45928_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : LJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 3...

EntireName: LJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
Components
  • Complex: LJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 35O22 Fab
    • Protein or peptide: 35O22 heavy chain Fv
    • Protein or peptide: 35O22 light chain Fv
    • Protein or peptide: LJF-085 heavy chain Fv
    • Protein or peptide: LJF-085 light chain Fv
    • Protein or peptide: HIV Env JRFL NFL TD CC3+ gp140
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: LJF-085 Fab in complex with HIV Env JRFL NFL TD CC3+ trimer and 3...

SupramoleculeName: LJF-085 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: 35O22 heavy chain Fv

MacromoleculeName: 35O22 heavy chain Fv / type: protein_or_peptide / ID: 1 / 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 #2: 35O22 light chain Fv

MacromoleculeName: 35O22 light chain Fv / type: protein_or_peptide / ID: 2 / 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 #3: LJF-085 heavy chain Fv

MacromoleculeName: LJF-085 heavy chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.593121 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSID DYFWNWVRQP PGKPLECIGY IFGRGGGTKY NPSLDNRVTI STDTPNQFSL KLRSVTVAD TAIYYCARWN LYDDDFGYNS FAVWGRGVLV TVSS

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Macromolecule #4: LJF-085 light chain Fv

MacromoleculeName: LJF-085 light chain Fv / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.850203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDTVT ITCQARHAVG KNLNWYQQKP GRGPQLLIYM ASSRHSGVPS RFRGSGSGRE FTLTINNLQP EDFATYSCQ QGYTYPWTFG QGTKVEMK

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Macromolecule #5: HIV Env JRFL NFL TD CC3+ gp140

MacromoleculeName: HIV Env JRFL NFL TD CC3+ gp140 / type: protein_or_peptide / ID: 5 / 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

UniProtKB: Envelope glycoprotein gp160

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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: 36 / 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

Concentration5.8 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: 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: 45.0 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64443
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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