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- EMDB-49411: AMC016 v4.2 in complex with pAb Base-A isolated from animal RQk18... -

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Basic information

Entry
Database: EMDB / ID: EMD-49411
TitleAMC016 v4.2 in complex with pAb Base-A isolated from animal RQk18 at week 43
Map data
Sample
  • Complex: AMC016 v4.2 in complex with Base-A pAb from animal RQk18 at week 43
    • Protein or peptide: RQk-Base-A pAb heavy chain
    • Protein or peptide: RQk-Base-A pAb light chain
    • Protein or peptide: AMC016v4.2 envelope glycoprotein gp120
    • Protein or peptide: AMC016v4.2 transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / polyclonal / cryoEMPEM / STRUCTURAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: bioRxiv / Year: 2024
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 / 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
DepositionFeb 24, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49411.png

Downloads & links

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Map

FileDownload / File: emd_49411.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 401.28 Å		1.05 Å/pix.
x 384 pix.
= 401.28 Å		1.05 Å/pix.
x 384 pix.
= 401.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.1300402 - 2.3482702
Average (Standard dev.)-0.0010548435 (±0.03438196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 401.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49411_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49411_half_map_2.map
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 Base-A pAb from animal RQk18 at week 43

EntireName: AMC016 v4.2 in complex with Base-A pAb from animal RQk18 at week 43
Components
  • Complex: AMC016 v4.2 in complex with Base-A pAb from animal RQk18 at week 43
    • Protein or peptide: RQk-Base-A pAb heavy chain
    • Protein or peptide: RQk-Base-A pAb light chain
    • Protein or peptide: AMC016v4.2 envelope glycoprotein gp120
    • Protein or peptide: AMC016v4.2 transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

SupramoleculeName: AMC016 v4.2 in complex with Base-A pAb from animal RQk18 at week 43
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 0.470 kDa/nm

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Macromolecule #1: RQk-Base-A pAb heavy chain

MacromoleculeName: RQk-Base-A pAb heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.234833 KDa
Recombinant expressionOrganism: Macaca mulatta (Rhesus monkey)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)W(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)W(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)W(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #2: RQk-Base-A pAb light chain

MacromoleculeName: RQk-Base-A pAb light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 9.068175 KDa
Recombinant expressionOrganism: Macaca mulatta (Rhesus monkey)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)W(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)W(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) F(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: AMC016v4.2 envelope glycoprotein gp120

MacromoleculeName: AMC016v4.2 envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.888934 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEEELWVTVY YGVPVWKEAT TTLFCASDAK AYDTEVHNVW ATHCCVPTDP SPQEVVLENV TENFNMWKNN MVEQMHEDII SLWDQSLKP CVKLTPLCVT LNCTDLGNAT DAINRNTTDA PNSTLRTMEE KGEIKNCSFN ITTSVRDKMQ KEYATFYKLD I VPIDNDNN ...String:
AEEELWVTVY YGVPVWKEAT TTLFCASDAK AYDTEVHNVW ATHCCVPTDP SPQEVVLENV TENFNMWKNN MVEQMHEDII SLWDQSLKP CVKLTPLCVT LNCTDLGNAT DAINRNTTDA PNSTLRTMEE KGEIKNCSFN ITTSVRDKMQ KEYATFYKLD I VPIDNDNN SYRLINCNTS VITQACPKVS FEPIPIHYCA PAGFAILKCN NKTFNGTGPC TNVSTVQCTH GIRPVVSTQL LL NGSLAEE EIVIRSENFT DNGKTIIVQL NESVEINCTR PNNNTRKSIH IGPGRAFYTT GQIIGNIRQA HCNISRAKWN NTL HKIVKK LREQFRNKTI VFKQSSGGDP EIVMHSFNCG GEFFYCNSTQ LFNSTWYGNE SSDNPGVEGN ITLPCRIKQI INLW QEVGK AMYAPPIGGQ IRCSSNITGL LLTRDGGNNN ITTEIFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTKCK RRVVQ

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Macromolecule #4: AMC016v4.2 transmembrane protein gp41

MacromoleculeName: AMC016v4.2 transmembrane protein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.192521 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RQLLSGIVQQ QSNLLRAPEC QQHLLKDTHW GIKQLQARVL AVEHYLKDQQ LLGIWGCSG KLICTTAVPW NATWSNKTLD NIWNNMTWME WEKEISNYTN LIYNLIEESQ NQQEKNETEN LTLC

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 49 / 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

BufferpH: 7.4
GridModel: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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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: 50.0 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: 0.8 µm
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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 357902
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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