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- EMDB-71881: 10E8-GT12 immunogen in complex with mouse Fabs SA2911 and W6-10 -

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Basic information

Entry
Database: EMDB / ID: EMD-71881
Title10E8-GT12 immunogen in complex with mouse Fabs SA2911 and W6-10
Map data
Sample
  • Complex: 10E8-GT12 immunogen in complex with mouse Fabs W6-10 and SA2911
    • Complex: W6-10 mouse Fab heavy and light chains
      • Protein or peptide: W6-10 mouse Fab heavy chain
      • Protein or peptide: W6-10 mouse Fab light chain
    • Complex: 10E8-GT12 immunogen
      • Protein or peptide: 10E8-GT12 immunogen
    • Complex: SA2911 mouse Fab heavy and light chains
      • Protein or peptide: SA2102_10E8-like_2911_H_pFabCW mouse Fab heavy chain
      • Protein or peptide: SA2102_Pro2621_10E8like2621_Kap_pCW mouse Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / 10E8 / Germline targeting / MPER / broadly neutralizing antibody / vaccine design / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 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: To Be Published
Title: Decipher antibody responses primed with scaffolds harboring the germline-targeting HIV Env MPER epitope by cryoEM
Authors: Huang J / Ward AB
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_71881.png

Downloads & links

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Map

FileDownload / File: emd_71881.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 366.52 Å		0.83 Å/pix.
x 440 pix.
= 366.52 Å		0.83 Å/pix.
x 440 pix.
= 366.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.1498802 - 2.1602983
Average (Standard dev.)-0.00042629326 (±0.02636245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 366.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71881_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71881_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71881_half_map_2.map
Projections & Slices
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Sample components

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Entire : 10E8-GT12 immunogen in complex with mouse Fabs W6-10 and SA2911

EntireName: 10E8-GT12 immunogen in complex with mouse Fabs W6-10 and SA2911
Components
  • Complex: 10E8-GT12 immunogen in complex with mouse Fabs W6-10 and SA2911
    • Complex: W6-10 mouse Fab heavy and light chains
      • Protein or peptide: W6-10 mouse Fab heavy chain
      • Protein or peptide: W6-10 mouse Fab light chain
    • Complex: 10E8-GT12 immunogen
      • Protein or peptide: 10E8-GT12 immunogen
    • Complex: SA2911 mouse Fab heavy and light chains
      • Protein or peptide: SA2102_10E8-like_2911_H_pFabCW mouse Fab heavy chain
      • Protein or peptide: SA2102_Pro2621_10E8like2621_Kap_pCW mouse Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 10E8-GT12 immunogen in complex with mouse Fabs W6-10 and SA2911

SupramoleculeName: 10E8-GT12 immunogen in complex with mouse Fabs W6-10 and SA2911
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: W6-10 mouse Fab heavy and light chains

SupramoleculeName: W6-10 mouse Fab heavy and light chains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: 10E8-GT12 immunogen

SupramoleculeName: 10E8-GT12 immunogen / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: SA2911 mouse Fab heavy and light chains

SupramoleculeName: SA2911 mouse Fab heavy and light chains / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: W6-10 mouse Fab heavy chain

MacromoleculeName: W6-10 mouse Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.161798 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPG ILQPSQTLSL TCSFSGFSLS TFGMGVGWIR QPSGKGLEWL AHIWWDDDKF YNPALKSRLT ISKDTSKNQV FLKIANVDT ADTATYYCAR IGEDYFLDVW GKGTTVTVSS

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Macromolecule #2: W6-10 mouse Fab light chain

MacromoleculeName: W6-10 mouse Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.657868 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPAS LSASVGETVT ITCRASGNIH NYLAWYQQKQ GKSPQLLVYN AKTLADGVPS RFSGSGSGTQ YSLKINSLQP EDFGSYYCQ HFWSAPYTFG GGTNLEIK

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Macromolecule #3: 10E8-GT12 immunogen

MacromoleculeName: 10E8-GT12 immunogen / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.384951 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ETGNVTQEDI IRALASPLIK DGMVDEDFAE KVIENESRYP SGLQAKGVGF AIPHVLGDYV RDNAISVGIL DKPVNFSEWY QSPDPVPVR VVFMLAIRTW DDITNVMNWI KDVVLDEEFM KRLLNMSDEE IYRQIYTRIS KAPNLSGINF SREYVRHLNG S GGSGLNDI FEAQKIEWHE GSGGHHHHHH

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Macromolecule #4: SA2102_10E8-like_2911_H_pFabCW mouse Fab heavy chain

MacromoleculeName: SA2102_10E8-like_2911_H_pFabCW mouse Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.118736 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLKQSGPG LVQPSQSLSI TCTVSGFSLT SYGVHWVRQS PGKGLEWLGV IWSGGSTDYN AAFISRLSIS KDNSKSQVFF KMNSLQADD TAIYYCARAP PYYDFWSGYS YYYYYMDVWG KGTTVTV

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Macromolecule #5: SA2102_Pro2621_10E8like2621_Kap_pCW mouse Fab light chain

MacromoleculeName: SA2102_Pro2621_10E8like2621_Kap_pCW mouse Fab light chain
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.323789 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPSS LAMSVGQKVT MSCKSSQSLL NSSNQKNYLA WYQQKPGQSP KLLVYFASTR ESGVPDRFIG SGSGTDFTLT ISSVQAEDL ADYFCQQHYS TPLTFGAGTK LELK

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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

Concentration2.9 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 KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.6 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
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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 171994
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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