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- EMDB-49412: AMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18... -

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Basic information

Entry
Database: EMDB / ID: EMD-49412
TitleAMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18 at week 43
Map dataBase 4 EM Map
Sample
  • Complex: AMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18 at week 43
    • Protein or peptide: RQk-Base-C pAb heavy chain
    • Protein or peptide: RQk-Base-C pAb light chain
    • Protein or peptide: AMC016 v4.2 gp120
    • Protein or peptide: AMC016 v4.2 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: 3.1 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_49412.png

Downloads & links

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Map

FileDownload / File: emd_49412.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBase 4 EM Map
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: 0.3
Minimum - Maximum-0.9382149 - 1.7852337
Average (Standard dev.)-0.0010886461 (±0.032173287)
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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Mask #1

Fileemd_49412_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49412_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_49412_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-C pAb isolated from animal RQk18...

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

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Supramolecule #1: AMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18...

SupramoleculeName: AMC016 v4.2 in complex with Base-C pAb isolated 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-C pAb heavy chain

MacromoleculeName: RQk-Base-C pAb heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 10.383783 KDa
SequenceString: (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) ...String:
(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)C(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)

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

MacromoleculeName: RQk-Base-C pAb light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 8.81286 KDa
SequenceString: (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) ...String:
(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: AMC016 v4.2 gp120

MacromoleculeName: AMC016 v4.2 gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 58.713809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEEEL WVTVYYGVPV WKEATTTLFC ASDAKAYDTE VHNVWATHCC VPTDPSPQE VVLENVTENF NMWKNNMVEQ MHEDIISLWD QSLKPCVKLT PLCVTLNCTD LGNATDAINR NTTDAPNSTL R TMEEKGEI ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEEEL WVTVYYGVPV WKEATTTLFC ASDAKAYDTE VHNVWATHCC VPTDPSPQE VVLENVTENF NMWKNNMVEQ MHEDIISLWD QSLKPCVKLT PLCVTLNCTD LGNATDAINR NTTDAPNSTL R TMEEKGEI KNCSFNITTS VRDKMQKEYA TFYKLDIVPI DNDNNSYRLI NCNTSVITQA CPKVSFEPIP IHYCAPAGFA IL KCNNKTF NGTGPCTNVS TVQCTHGIRP VVSTQLLLNG SLAEEEIVIR SENFTDNGKT IIVQLNESVE INCTRPNNNT RKS IHIGPG RAFYTTGQII GNIRQAHCNI SRAKWNNTLH KIVKKLREQF RNKTIVFKQS SGGDPEIVMH SFNCGGEFFY CNST QLFNS TWYGNESSDN PGVEGNITLP CRIKQIINLW QEVGKAMYAP PIGGQIRCSS NITGLLLTRD GGNNNITTEI FRPGG GDMR DNWRSELYKY KVVKIEPLGV APTKCKRRVV QRRRRRR

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Macromolecule #4: AMC016 v4.2 gp41

MacromoleculeName: AMC016 v4.2 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: 42 / 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
Component:
ConcentrationName
50.0 mMTris
150.0 mMSodium Chrlode
0.005 mMLauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 142407
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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