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- EMDB-49457: BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isola... -

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Basic information

Entry
Database: EMDB / ID: EMD-49457
TitleBG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isolated from animal RUu18 at week 14
Map dataEM Main Map Base 1 RUu18
Sample
  • Complex: BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isolated from animal RUu18 at week 14
    • Complex: BG505-CH505 Env glycoprotein
      • Protein or peptide: BG505-CH505 Envelope glycoprotein gp120
      • Protein or peptide: BG505-CH505 Transmembrane protein gp41
    • Complex: pAb Base-1
      • Protein or peptide: RUu-Base-1 pAb heavy chain
      • Protein or peptide: RUu-Base-1 pAb light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / polyclonal / cryoEMPEM / STRUCTURAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 25, 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_49457.png

Downloads & links

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Map

FileDownload / File: emd_49457.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM Main Map Base 1 RUu18
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 416 pix.
= 478.4 Å		1.15 Å/pix.
x 416 pix.
= 478.4 Å		1.15 Å/pix.
x 416 pix.
= 478.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.82094324 - 1.5527679
Average (Standard dev.)-0.0006869476 (±0.0258171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 478.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49457_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_49457_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_49457_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 : BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isola...

EntireName: BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isolated from animal RUu18 at week 14
Components
  • Complex: BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isolated from animal RUu18 at week 14
    • Complex: BG505-CH505 Env glycoprotein
      • Protein or peptide: BG505-CH505 Envelope glycoprotein gp120
      • Protein or peptide: BG505-CH505 Transmembrane protein gp41
    • Complex: pAb Base-1
      • Protein or peptide: RUu-Base-1 pAb heavy chain
      • Protein or peptide: RUu-Base-1 pAb light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isola...

SupramoleculeName: BG505-CH505 Env glycoprotein in complex with NHP pAb Base-1 isolated from animal RUu18 at week 14
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: BG505-CH505 Env glycoprotein

SupramoleculeName: BG505-CH505 Env glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: pAb Base-1

SupramoleculeName: pAb Base-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: RUu-Base-1 pAb heavy chain

MacromoleculeName: RUu-Base-1 pAb heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 10.639099 KDa
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)(UNK)(UNK)W(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)(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) C(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: RUu-Base-1 pAb light chain

MacromoleculeName: RUu-Base-1 pAb light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 9.153279 KDa
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) (UNK)F (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #3: BG505-CH505 Envelope glycoprotein gp120

MacromoleculeName: BG505-CH505 Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.228031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHCCV PTDPNPQEI VLENVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCTNA TASNSSIIEG MKNCSFNITT E LRDKREKK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHCCV PTDPNPQEI VLENVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCTNA TASNSSIIEG MKNCSFNITT E LRDKREKK NALFYKLDIV QLDGNSSQYR LINCNTSAIT QACPKVSFEP IPIHYCAPAG FAILKCNNKT FTGTGPCNNV ST VQCTHGI KPVVSTQLLL NGSLAEGEII IRSENITDNG KTILVHLNES VKIECTRPNN KTRTSIRIGP GQAFYATGQV IGD IREAYC NISESTWNET LGKVVKQLRK HFPHKNITFQ PSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWISNTSVQ GSNS TGSND SITLPCRIKQ IINMWQEVGR AMYAPPIQGN ITCVSNITGL ILTRDGGKNN TETFRPGGGD MRDNWRSELY KYKVV KIEP LGVAPTACKR RVVGRRRRRR

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Macromolecule #4: BG505-CH505 Transmembrane protein gp41

MacromoleculeName: BG505-CH505 Transmembrane protein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.16535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEC QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICTTNVPW NSTWSNKTLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNETDN LTCD

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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: 40 / 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
50.0 mMSodium Chloride
0.005 mMLauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 7167 / Average electron dose: 49.92 e/Å2
Electron beamAcceleration voltage: 200 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 / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 181253
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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