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- EMDB-72068: RQk18_FP_mAb_05 in complex with AMC016 and PGT122 -

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Basic information

Entry
Database: EMDB / ID: EMD-72068
TitleRQk18_FP_mAb_05 in complex with AMC016 and PGT122
Map datamain map
Sample
  • Complex: AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43
    • Other: AMC016 gp120
    • Other: AMC016 gp41
    • Other: RQk-FP-mAb 05 Fab Heavy Chain
    • Other: RQk-FP-mAb 05 Fab Light Chain
    • Other: PGT122 Fab Heavy Chain
    • Other: PGT122 Fab Light Chain
KeywordsHIV-1 / polyclonal / cryoEMPEM / STRUCTURAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPratap PP / 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)R01 AI145629 United States
CitationJournal: NPJ Vaccines / Year: 2025
Title: Immunofocusing on the conserved fusion peptide of HIV envelope glycoprotein in rhesus macaques.
Authors: Payal P Pratap / Christopher A Cottrell / James Quinn / Diane G Carnathan / Daniel L V Bader / Andy S Tran / Chiamaka A Enemuo / Julia T Ngo / Sara T Richey / Hongmei Gao / Xiaoying Shen / ...Authors: Payal P Pratap / Christopher A Cottrell / James Quinn / Diane G Carnathan / Daniel L V Bader / Andy S Tran / Chiamaka A Enemuo / Julia T Ngo / Sara T Richey / Hongmei Gao / Xiaoying Shen / Kelli M Greene / Jonathan Hurtado / Katarzyna Kaczmarek Michaels / Elana Ben-Akiva / Ashley Lemnios / Mariane B Melo / Joel D Allen / Gabriel Ozorowski / Max Crispin / Bryan Briney / David Montefiori / Guido Silvestri / Darrell J Irvine / Shane Crotty / Andrew B Ward /
Abstract: During infection, the fusion peptide (FP) of HIV envelope glycoprotein (Env) serves a central role in viral fusion with the host cell. As such, the FP is highly conserved and therefore an attractive ...During infection, the fusion peptide (FP) of HIV envelope glycoprotein (Env) serves a central role in viral fusion with the host cell. As such, the FP is highly conserved and therefore an attractive epitope for vaccine design. Here, we describe a vaccination study in non-human primates (NHPs) where glycan deletions were made on soluble HIV Env to increase FP epitope exposure. When delivered via implantable osmotic pumps, this immunogen primed immune responses against the FP, which were then boosted with heterologous trimers resulting in a focused immune response targeting the conserved FP epitope. Although autologous immunizations did not elicit high affinity FP-targeting antibodies, the conserved FP epitope on a heterologous trimer further matured the lower affinity, FP-targeting B cells. This study suggests using epitope conservation strategies on distinct Env trimer immunogens can focus humoral responses on desired neutralizing epitopes and suppress immune-distracting antibody responses against non-neutralizing epitopes.
History
DepositionAug 10, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72068.png

Downloads & links

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Map

FileDownload / File: emd_72068.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.)
1.04 Å/pix.
x 400 pix.
= 417.6 Å		1.04 Å/pix.
x 400 pix.
= 417.6 Å		1.04 Å/pix.
x 400 pix.
= 417.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.044 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5259317 - 0.7415235
Average (Standard dev.)-0.00020329555 (±0.012660348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 417.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72068_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72068_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_72068_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43

EntireName: AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43
Components
  • Complex: AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43
    • Other: AMC016 gp120
    • Other: AMC016 gp41
    • Other: RQk-FP-mAb 05 Fab Heavy Chain
    • Other: RQk-FP-mAb 05 Fab Light Chain
    • Other: PGT122 Fab Heavy Chain
    • Other: PGT122 Fab Light Chain

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Supramolecule #1: AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43

SupramoleculeName: AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: AMC016 gp120

MacromoleculeName: AMC016 gp120 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEEEL WVTVYYGVPV WKEATTTLFC ASDAKAYDTE VHNVWATHCC VPTDPSPQEV VLENVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCTDL GNATDAINRN TTDAPNSTLR TMEEKGEIKN ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEEEL WVTVYYGVPV WKEATTTLFC ASDAKAYDTE VHNVWATHCC VPTDPSPQEV VLENVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCTDL GNATDAINRN TTDAPNSTLR TMEEKGEIKN CSFNITTSVR DKMQKEYATF YKLDIVPIDN DNNSYRLINC NTSVITQACP KVSFEPIPIH YCAPAGFAIL KCNNKTFNGT GPCTNVSTVQ CTHGIRPVVS TQLLLNGSLA EEEIVIRSEN FTDNGKTIIV QLNESVEINC TRPNNNTRKS IHIGPGRAFY TTGQIIGNIR QAHCNISRAK WNNTLHKIVK KLREQFRNKT IVFKQSSGGD PEIVMHSFNC GGEFFYCNST QLFNSTWYGN ESSDNPGVEG NITLPCRIKQ IINLWQEVGK AMYAPPIGGQ IRCSSNITGL LLTRDGGNNN ITTEIFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTKCK RRVVQRRRRR R

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Macromolecule #2: AMC016 gp41

MacromoleculeName: AMC016 gp41 / type: other / ID: 2 / Classification: other
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RQLLSGIVQQ QSNLLRAPEC QQHLLKDTHW GIKQLQARVL AVEHYLKDQQ LLGIWGCSGK LICTTAVPWN ATWSNKTLDN IWNNMTWMEW EKEISNYTNL IYNLIEESQN QQEKNETENL TLC

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Macromolecule #3: RQk-FP-mAb 05 Fab Heavy Chain

MacromoleculeName: RQk-FP-mAb 05 Fab Heavy Chain / type: other / ID: 3 / Classification: other
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGGKFS SNWWGWIRQP PGKGLEWIGY VYGGSGYTEY NPSLRSRATI SRDLSTDHFS LKLDSVTAAD TAVYFCARAP RRLYRDGRYD YGNFDYWGQG VLVTVSS

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Macromolecule #4: RQk-FP-mAb 05 Fab Light Chain

MacromoleculeName: RQk-FP-mAb 05 Fab Light Chain / type: other / ID: 4 / Classification: other
SequenceString:
DIQMSQSPSS LSASVGDRVT ITCRASQGIS NYLAWYQQKP GKAPKLLIYK ASTLASGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQQ HNSNPPTFGG GTKLDIK

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Macromolecule #5: PGT122 Fab Heavy Chain

MacromoleculeName: PGT122 Fab Heavy Chain / type: other / ID: 5 / Classification: other
SequenceString: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAADS AIYYCATTKH GRRIYGVVAF KEWFTYFYMD VWGKGTSVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT ...String:
QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAADS AIYYCATTKH GRRIYGVVAF KEWFTYFYMD VWGKGTSVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSC

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Macromolecule #6: PGT122 Fab Light Chain

MacromoleculeName: PGT122 Fab Light Chain / type: other / ID: 6 / Classification: other
SequenceString: APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWDS RRPTNWVFGE GTTLIVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV ETTTPSKQSN ...String:
APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWDS RRPTNWVFGE GTTLIVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV ETTTPSKQSN NKYAASSYLS LTPEQWKSHK SYSCQVTHEG STVEKTVAPT ECS

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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
Component:
ConcentrationName
50.0 mMTris
150.0 mMSodium Chloride
0.005 %w/vLauryl Maltose Neopentyl Glycol
GridModel: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.29 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v0r

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111683
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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