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- EMDB-45957: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-45957
TitleLJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer
Map datamain map
Sample
  • Complex: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer
    • Protein or peptide: ZM233 NFL TD CC3+ gp140
    • Protein or peptide: LJF-085 heavy chain Fv
    • Protein or peptide: LJF-085 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 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 28, 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_45957.png

Downloads & links

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Map

FileDownload / File: emd_45957.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 400 pix.
= 402.08 Å		1.01 Å/pix.
x 400 pix.
= 402.08 Å		1.01 Å/pix.
x 400 pix.
= 402.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.19383305 - 0.3910602
Average (Standard dev.)0.000079543075 (±0.010927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 402.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45957_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_45957_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_45957_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer

EntireName: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer
Components
  • Complex: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer
    • Protein or peptide: ZM233 NFL TD CC3+ gp140
    • Protein or peptide: LJF-085 heavy chain Fv
    • Protein or peptide: LJF-085 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer

SupramoleculeName: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: ZM233 NFL TD CC3+ gp140

MacromoleculeName: ZM233 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: 73.305516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAMGSLWV TVYYGVPVWR DAETTLFCAS DAKAYETEKH SVWATHACVP TDPNPQEMVL ENVTENFNM WKNDMVDQMH TDVISIWDQS LKPCVKLTPL CVTLDCSTYN NTHNISKEMK ICSFNMTTEL RDKKRKVNVL F YKLDLVPL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAMGSLWV TVYYGVPVWR DAETTLFCAS DAKAYETEKH SVWATHACVP TDPNPQEMVL ENVTENFNM WKNDMVDQMH TDVISIWDQS LKPCVKLTPL CVTLDCSTYN NTHNISKEMK ICSFNMTTEL RDKKRKVNVL F YKLDLVPL TNSSNTTNYR LISCNTSTIT QACPKVSFDP IPIHYCAPAG YAILKCNNKT FNGTGPCNNV STVQCTHGIK PV VSTQLLL NGSLAEEEII IRFENLTDNV KIIIVQLNET INITCTRPNN YTRKSIRIGP GQSFYAMGEI VGNIREAHCN ISA SKWNKT LERVRTKLKE HFPNKTIEFE PSSGGDLEIT THSFNCGGEF FYCNTSGLFN SAINGTLTSN VTLPCRIKQI INMW QRVGQ AMYAPPIAGN ITCKSNITGL LLTRDGGENS SSTTETFRPT GGDMKNNWRS ELYKYKVVEI KPLGIAPTRC KRRVV EGGG GSGGGGSAVG IGAVRRGFLG AAGSTMGAAS MTLTVQARQL LSGIVQPQSN LLKAPEAQQH MLQLGVWGIK QLQARV LAI ERYLKDQQLL GLWGCSGKLI CTTNVPWNAS WSNKSKNDIW DNMTWMQWDR EIGNHTDTIY RLLEDSQNQQ EKNEKDL LC LDGGGGSHHH HHHHHGSGC

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Macromolecule #2: LJF-085 heavy chain Fv

MacromoleculeName: LJF-085 heavy chain Fv / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: LJF-085 light chain Fv

MacromoleculeName: LJF-085 light chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 30 / 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

Concentration1 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris pH 7.4, 150 mM NaCl, 0.005 mM LMNG
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34340
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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