[English] 日本語
Yorodumi
- EMDB-49417: BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 iso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49417
TitleBG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 isolated from animal RUu18 at week 14
Map dataEM Map V1V2V3-2
Sample
  • Complex: BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 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 V1V2V3-2
      • Protein or peptide: RUu-V1V2V3-2 pAb heavy chain
      • Protein or peptide: RUu-V1V2V3-2 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: 3.9 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: 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

-
Structure visualization

Supplemental images

emd_49417.png

Downloads & links

-
Map

FileDownload / File: emd_49417.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM Map V1V2V3-2
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: 0.36
Minimum - Maximum-0.8961309 - 1.5585091
Average (Standard dev.)-0.000684553 (±0.03234259)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_49417_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_49417_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_49417_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 iso...

EntireName: BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 isolated from animal RUu18 at week 14
Components
  • Complex: BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 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 V1V2V3-2
      • Protein or peptide: RUu-V1V2V3-2 pAb heavy chain
      • Protein or peptide: RUu-V1V2V3-2 pAb light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 iso...

SupramoleculeName: BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 isolated from animal RUu18 at week 14
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

-
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

-
Supramolecule #3: pAb V1V2V3-2

SupramoleculeName: pAb V1V2V3-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Macromolecule #1: RUu-V1V2V3-2 pAb heavy chain

MacromoleculeName: RUu-V1V2V3-2 pAb heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 10.724203 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)W(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)(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)(UNK)(UNK)

-
Macromolecule #2: RUu-V1V2V3-2 pAb light chain

MacromoleculeName: RUu-V1V2V3-2 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)(UNK) C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) W(UNK)(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)(UNK) C(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)

-
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

-
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

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 47 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationName
50.0 mMTris
50.0 mMSodium Chloride
0.005 mMLauryl Maltose Neopentyl Glycol
VitrificationCryogen name: ETHANE

-
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

+
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: 87728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more