[English] 日本語
Yorodumi
- EMDB-71782: Cryo-EM structure of HIV-1 459C-ALT DS-SOSIP RnS Env trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71782
TitleCryo-EM structure of HIV-1 459C-ALT DS-SOSIP RnS Env trimer
Map data
Sample
  • Complex: HIV-1 Env 459C-ALT RnS DS-SOSIP
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp41
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEnvelope trimer / 459C-ALT / RnS DS-SOSIP immunogen / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsWang S / Zhou T / Kwong PD / Morano NC / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2026
Title: Vaccine elicitation of HIV-1 neutralizing antibodies against both V2 apex and fusion peptide in rhesus macaques.
Authors: Hongying Duan / Joseph P Nkolola / Shuishu Wang / Jayeshbhai Chaudhari / I-Ting Teng / Christy Lavine / Danealle K Parchment / George S Sellers / Krisha McKee / Sijy O'Dell / Misook Choe / ...Authors: Hongying Duan / Joseph P Nkolola / Shuishu Wang / Jayeshbhai Chaudhari / I-Ting Teng / Christy Lavine / Danealle K Parchment / George S Sellers / Krisha McKee / Sijy O'Dell / Misook Choe / Haijuan Du / Baoshan Zhang / Alejandro A Espinosa Perez / Annika Rossler / Ninaad Lasrado / Andrea Biju / Jordan E Becker / Robin Carroll / Audrey S Carson / Amy R Henry / Nicholas C Morano / Madeeha Mughal / Reda Rawi / Ryan S Roark / Chaim A Schramm / Chen-Hsiang Shen / Sarah C Smith / Tyler Stephens / Yaroslav Tsybovsky / David J Van Wazer / Hua Wang / Yongping Yang / Lucy Rutten / Johannes P M Langedijk / Cheng Cheng / Lingshu Wang / Daniel C Douek / Richard A Koup / John R Mascola / Lawrence Shapiro / Tongqing Zhou / Nicole A Doria-Rose / Bette Korber / Michael S Seaman / Theodore C Pierson / Peter D Kwong / Dan H Barouch /
Abstract: Broadly neutralizing antibodies (bNAbs) targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of bNAbs against multiple epitopes has not been ...Broadly neutralizing antibodies (bNAbs) targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of bNAbs against multiple epitopes has not been achieved by vaccination. In this study, we designed a dual-epitope vaccine targeting both the fusion peptide (FP) and the V2 apex and evaluated its capacity to induce bNAbs against both epitopes in rhesus macaques. This vaccine combined an FP conjugate with a cocktail of engineered Env trimers with enhanced V2 apex recognition and increased antigen retention in lymph nodes. Macaque immunization with the dual-epitope vaccine elicited >1,000-fold higher autologous tier 2-neutralizing titers than wild-type Env trimers and enhanced heterologous neutralization. Both FP- and V2 apex-monoclonal antibodies were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures similar to well-characterized FP and V2 apex bNAbs. These results demonstrate proof of concept for simultaneous vaccine elicitation of neutralizing antibodies against multiple sites of Env vulnerability.
History
DepositionJul 22, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71782.png

Downloads & links

-
Map

FileDownload / File: emd_71782.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 356.4 Å		0.83 Å/pix.
x 432 pix.
= 356.4 Å		0.83 Å/pix.
x 432 pix.
= 356.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275
Minimum - Maximum-0.105617076 - 0.24857686
Average (Standard dev.)0.00019075423 (±0.0075267553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 356.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_71782_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_71782_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-1 Env 459C-ALT RnS DS-SOSIP

EntireName: HIV-1 Env 459C-ALT RnS DS-SOSIP
Components
  • Complex: HIV-1 Env 459C-ALT RnS DS-SOSIP
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp41
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: HIV-1 Env 459C-ALT RnS DS-SOSIP

SupramoleculeName: HIV-1 Env 459C-ALT RnS DS-SOSIP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

-
Macromolecule #1: HIV-1 459C-ALT RnS DS-SOSIP gp41

MacromoleculeName: HIV-1 459C-ALT RnS DS-SOSIP gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.137424 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLPKAPEA QQHLLQLTVW GIKQLQTRVL AIERYLEVQQ LLGLWGCSG KLICCTAVPW NSSWSNKSET EIWNNMTWMQ WDREISNYTN TIYRLLEESQ FQQEINEVDL LALD

-
Macromolecule #2: HIV-1 459C-ALT RnS DS-SOSIP gp120

MacromoleculeName: HIV-1 459C-ALT RnS DS-SOSIP gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.049219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNLWVTVYYG VPVWREAETT LFCASDAKAY DREVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNDMV DQMHEDIISL WDQSLKPCV KLTPLCVTLD CKAFNSSSHT NSSIAMQEMK NCTFNITTSV KGKRQQEHAL FYKLDIVPLN KNGRQYRLIN C NTSTITQA ...String:
GNLWVTVYYG VPVWREAETT LFCASDAKAY DREVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNDMV DQMHEDIISL WDQSLKPCV KLTPLCVTLD CKAFNSSSHT NSSIAMQEMK NCTFNITTSV KGKRQQEHAL FYKLDIVPLN KNGRQYRLIN C NTSTITQA CPKVSFDPIP IHYCTPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEEDIIIRS EN LTNNAKT IIVHLNESVE IVCVRPNNMT RKSIRIGPGQ TFYALNEIIG DIRQAHCNIS KEKWNNTLHR VWKKLVEHFP NKT TIRFDR HSGGDLEITT HSFNCGGEFF YCNTSGLFNI TYNSNYTYND TKHNGTKVIT LPCRIKQIIN MWQEVGRAMY APPI AGNIT CTSNITGLLL TRDGGNNSTE TETFRPGGGD MRDNWRSELY KYKVVEIKPL GIAPTGCKRR VVER

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 15 / 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 / Details: PBS + 0.005% (w/v) DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fr6

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 158204
Initial angle assignmentType: NOT APPLICABLE / Software - Name: UCSF ChimeraX (ver. 1.9)
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9pq3:
Cryo-EM structure of HIV-1 459C-ALT DS-SOSIP RnS Env trimer

+
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