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- EMDB-71883: 10E8-GT10.2 immunogen in complex with Rhesus macaque Fab W3-05 an... -

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Basic information

Entry
Database: EMDB / ID: EMD-71883
Title10E8-GT10.2 immunogen in complex with Rhesus macaque Fab W3-05 and mouse Fab W6-03
Map data
Sample
  • Complex: 10E8-GT10.2 immunogen in complex with mouse Fab W6-03 and rhesus macaque Fab W3-05
    • Complex: W6-03 mouse Fab heavy chain, W6-03 mouse Fab light chain
      • Protein or peptide: W6-03 mouse Fab heavy chain
      • Protein or peptide: W6-03 mouse Fab light chain
    • Complex: 10E8-GT10.2 immunogen
      • Protein or peptide: 10E8-GT10.2 immunogen
    • Complex: W3-05 rhesus macaque Fab heavy chain, W3-05 rhesus macaque Fab light chain
      • Protein or peptide: W3-05 rhesus macaque Fab heavy chain
      • Protein or peptide: W3-05 rhesus macaque Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / Germline targeting / MPER / broadly neutralizing antibody / vaccine design / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMus musculus (house mouse) / synthetic construct (others) / Homo sapiens (human) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHuang J / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002916 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: Nat Immunol / Year: 2024
Title: Vaccination induces broadly neutralizing antibody precursors to HIV gp41.
Authors: Torben Schiffner / Ivy Phung / Rashmi Ray / Adriana Irimia / Ming Tian / Olivia Swanson / Jeong Hyun Lee / Chang-Chun D Lee / Ester Marina-Zárate / So Yeon Cho / Jiachen Huang / Gabriel ...Authors: Torben Schiffner / Ivy Phung / Rashmi Ray / Adriana Irimia / Ming Tian / Olivia Swanson / Jeong Hyun Lee / Chang-Chun D Lee / Ester Marina-Zárate / So Yeon Cho / Jiachen Huang / Gabriel Ozorowski / Patrick D Skog / Andreia M Serra / Kimmo Rantalainen / Joel D Allen / Sabyasachi Baboo / Oscar L Rodriguez / Sunny Himansu / Jianfu Zhou / Jonathan Hurtado / Claudia T Flynn / Katherine McKenney / Colin Havenar-Daughton / Swati Saha / Kaitlyn Shields / Steven Schultze / Melissa L Smith / Chi-Hui Liang / Laura Toy / Simone Pecetta / Ying-Cing Lin / Jordan R Willis / Fabian Sesterhenn / Daniel W Kulp / Xiaozhen Hu / Christopher A Cottrell / Xiaoya Zhou / Jennifer Ruiz / Xuesong Wang / Usha Nair / Kathrin H Kirsch / Hwei-Ling Cheng / Jillian Davis / Oleksandr Kalyuzhniy / Alessia Liguori / Jolene K Diedrich / Julia T Ngo / Vanessa Lewis / Nicole Phelps / Ryan D Tingle / Skye Spencer / Erik Georgeson / Yumiko Adachi / Michael Kubitz / Saman Eskandarzadeh / Marc A Elsliger / Rama R Amara / Elise Landais / Bryan Briney / Dennis R Burton / Diane G Carnathan / Guido Silvestri / Corey T Watson / John R Yates / James C Paulson / Max Crispin / Gevorg Grigoryan / Andrew B Ward / Devin Sok / Frederick W Alt / Ian A Wilson / Facundo D Batista / Shane Crotty / William R Schief /
Abstract: A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design ...A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.
History
DepositionAug 1, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71883.png

Downloads & links

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Map

FileDownload / File: emd_71883.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 416 pix.
= 301.6 Å		0.73 Å/pix.
x 416 pix.
= 301.6 Å		0.73 Å/pix.
x 416 pix.
= 301.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.37789443 - 0.45516133
Average (Standard dev.)0.00011268556 (±0.009307613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 301.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71883_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_71883_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71883_half_map_2.map
Projections & Slices
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Sample components

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Entire : 10E8-GT10.2 immunogen in complex with mouse Fab W6-03 and rhesus ...

EntireName: 10E8-GT10.2 immunogen in complex with mouse Fab W6-03 and rhesus macaque Fab W3-05
Components
  • Complex: 10E8-GT10.2 immunogen in complex with mouse Fab W6-03 and rhesus macaque Fab W3-05
    • Complex: W6-03 mouse Fab heavy chain, W6-03 mouse Fab light chain
      • Protein or peptide: W6-03 mouse Fab heavy chain
      • Protein or peptide: W6-03 mouse Fab light chain
    • Complex: 10E8-GT10.2 immunogen
      • Protein or peptide: 10E8-GT10.2 immunogen
    • Complex: W3-05 rhesus macaque Fab heavy chain, W3-05 rhesus macaque Fab light chain
      • Protein or peptide: W3-05 rhesus macaque Fab heavy chain
      • Protein or peptide: W3-05 rhesus macaque Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 10E8-GT10.2 immunogen in complex with mouse Fab W6-03 and rhesus ...

SupramoleculeName: 10E8-GT10.2 immunogen in complex with mouse Fab W6-03 and rhesus macaque Fab W3-05
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: W6-03 mouse Fab heavy chain, W6-03 mouse Fab light chain

SupramoleculeName: W6-03 mouse Fab heavy chain, W6-03 mouse Fab light chain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: 10E8-GT10.2 immunogen

SupramoleculeName: 10E8-GT10.2 immunogen / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: W3-05 rhesus macaque Fab heavy chain, W3-05 rhesus macaque Fab li...

SupramoleculeName: W3-05 rhesus macaque Fab heavy chain, W3-05 rhesus macaque Fab light chain
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 10E8-GT10.2 immunogen

MacromoleculeName: 10E8-GT10.2 immunogen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.828348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TGNVTQEDII RALASPLIKD GMVDEDFAEY VIARENRSPT GLQAKGVGVA IPHTLGDYVR DNAISVGILD KPVNFSGWYQ SPDPVPVRV VFMLAGRTWD DIVIVLKWIK DVILDEEFMK RLLNMSDEEI YRQIYTRISK APNLSGINFS REYVRHLN

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Macromolecule #2: W6-03 mouse Fab heavy chain

MacromoleculeName: W6-03 mouse Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.537935 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVQLQESGPG LVKPSQSLSL TCSVTGYSIT SGYYWNWIRQ FPGNKLEWMG YISYDGSNNY NPSLKNRISI TRDTSQNQFF LKLNSVTTE DTASYYCARE GPYYDFWSGY YAYYMDVWGK GTTVTVSS

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Macromolecule #3: W6-03 mouse Fab light chain

MacromoleculeName: W6-03 mouse Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.410997 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMSQSPSS LAVSVGEKVT MSCKSSQSLL YSSNQKNYLA WYQQKPGQSP KLLIYWASTR KSGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYFG YPLTFGAGTK LELK

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Macromolecule #4: W3-05 rhesus macaque Fab heavy chain

MacromoleculeName: W3-05 rhesus macaque Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.34599 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS NYWMSWVRQA PGKGLEWVGF IKNKADGGTA AYAESVKGRF TISRDDSKNT LYLQMNSLK TEDTAVYYCA RDLGRYNFWS GFYSQNRFDV WGPGVLVTVS S

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Macromolecule #5: W3-05 rhesus macaque Fab light chain

MacromoleculeName: W3-05 rhesus macaque Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.580653 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYEVTQPPSV SVSPGQMARI TCGGDNLGSK YVHWYQQKPA QAPVLVIYDD SERPSGIPER FSGSKSGNTA TLTISGVEAG DEADYYCQV WDSSSDHPLF GGGTRLTVL

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / 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

Concentration4.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMTris
150.0 mMsodium chloride
0.005 mMLauryl Maltose Neopentyl Glycol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: Cryosparc Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 41951
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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