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- EMDB-72108: Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72108
TitleCryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
Map data
Sample
  • Complex: BG505 DS-SOSIP DFPH-a.01_10R59P_LC FAB COMPLEX
    • Complex: BG505 DS-SOSIP
      • Protein or peptide: HIV-1 BG505 DS-SOSIP gp120
      • Protein or peptide: BG505 DS-SOSIP GP41
    • Complex: DFPH-a.01_10R59P_LC FAB
      • Protein or peptide: DFPH-a.01_10R59P_LC Fab heavy chain
      • Protein or peptide: DFPH-a.01_10R59P_LC Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody improvement / broadly neutralizing antibody / epitope / fusion peptide / HIV-1 vaccine / paratope / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca (macaques)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPletnev S / Kwong P / Fischer E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Vaccines (Basel) / Year: 2025
Title: Yeast Display Reveals Plentiful Mutations That Improve Fusion Peptide Vaccine-Elicited Antibodies Beyond 59% HIV-1 Neutralization Breadth.
Authors: Camila T França / Sergei Pletnev / Bharat Madan / Phinikoula S Katsamba / Krisha McKee / Nicholas C Morano / Baoshan Zhang / Fabiana Bahna / Tatsiana Bylund / Bob C Lin / Mark K Louder / ...Authors: Camila T França / Sergei Pletnev / Bharat Madan / Phinikoula S Katsamba / Krisha McKee / Nicholas C Morano / Baoshan Zhang / Fabiana Bahna / Tatsiana Bylund / Bob C Lin / Mark K Louder / Seetha Mannepalli / Rajani Nimrania / Sijy O'Dell / Nicole A Doria-Rose / Peter D Kwong / Lawrence Shapiro / Zizhang Sheng / Tongqing Zhou / Brandon J DeKosky /
Abstract: : Vaccine elicitation of antibodies with high HIV-1 neutralization breadth is a long-standing goal. Recently, the induction of such antibodies has been achieved at the fusion peptide site of ...: Vaccine elicitation of antibodies with high HIV-1 neutralization breadth is a long-standing goal. Recently, the induction of such antibodies has been achieved at the fusion peptide site of vulnerability. Questions remain, however, as to how much anti-fusion peptide antibodies can be improved and whether their neutralization breadth and potency are sufficient to prevent HIV-1 infection. : Here, we use yeast display coupled with deep mutational screening and biochemical and structural analyses to study the improvement of the best fusion peptide-directed, vaccine-elicited antibody, DFPH_a.01, with an initial 59% breadth. : Yeast display identified both single and double mutations that improved recognition of HIV-1 envelope trimers. We characterized two paratope-distal light chain (LC) mutations, S10R and S59P, which together increased breadth to 63%. Biochemical analysis demonstrated DFPH-a.01_10R59P-LC, and its component mutations, to have increased affinity and stability. Cryo-EM structural analysis revealed elbow-angle influencing by S10R-LC and isosteric positioning by S59P-LC as explanations for enhanced breadth, affinity, and stability. : These results, along with another antibody with enhanced performance (DFPH-a.01_1G10A56K-LC with 64% breadth), suggest that mutations improving DFPH_a.01 are plentiful, an important vaccine insight.
History
DepositionAug 13, 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_72108.png

Downloads & links

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Map

FileDownload / File: emd_72108.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.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-1.1146951 - 1.6787921
Average (Standard dev.)0.00021094464 (±0.03072781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 365.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72108_msk_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72108_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_72108_half_map_2.map
Projections & Slices
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Sample components

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Entire : BG505 DS-SOSIP DFPH-a.01_10R59P_LC FAB COMPLEX

EntireName: BG505 DS-SOSIP DFPH-a.01_10R59P_LC FAB COMPLEX
Components
  • Complex: BG505 DS-SOSIP DFPH-a.01_10R59P_LC FAB COMPLEX
    • Complex: BG505 DS-SOSIP
      • Protein or peptide: HIV-1 BG505 DS-SOSIP gp120
      • Protein or peptide: BG505 DS-SOSIP GP41
    • Complex: DFPH-a.01_10R59P_LC FAB
      • Protein or peptide: DFPH-a.01_10R59P_LC Fab heavy chain
      • Protein or peptide: DFPH-a.01_10R59P_LC Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 DS-SOSIP DFPH-a.01_10R59P_LC FAB COMPLEX

SupramoleculeName: BG505 DS-SOSIP DFPH-a.01_10R59P_LC FAB COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: BG505 DS-SOSIP

SupramoleculeName: BG505 DS-SOSIP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: DFPH-a.01_10R59P_LC FAB

SupramoleculeName: DFPH-a.01_10R59P_LC FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Macaca (macaques)

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Macromolecule #1: HIV-1 BG505 DS-SOSIP gp120

MacromoleculeName: HIV-1 BG505 DS-SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.086324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: BG505 DS-SOSIP GP41

MacromoleculeName: BG505 DS-SOSIP GP41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: DFPH-a.01_10R59P_LC Fab heavy chain

MacromoleculeName: DFPH-a.01_10R59P_LC Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 24.875758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQVSGPG VVKASETLSL TCDVSSASNT RDYFYWSWVR QSPGKGLEWI GGVYSNSDTS NKNPSLESRV TISKDTSKNR FFLRLNSVT AADTAVYYCS SRAKIYFAVG YDSGGRIDVW GPGVLVTVAT ASTKGPSVFP LAPSSRSTSE STAALGCLVK D YFPEPVTV ...String:
QVQLQVSGPG VVKASETLSL TCDVSSASNT RDYFYWSWVR QSPGKGLEWI GGVYSNSDTS NKNPSLESRV TISKDTSKNR FFLRLNSVT AADTAVYYCS SRAKIYFAVG YDSGGRIDVW GPGVLVTVAT ASTKGPSVFP LAPSSRSTSE STAALGCLVK D YFPEPVTV SWNSGSLTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYVCNVNHKP SNTKVDKRVE IKTCG

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Macromolecule #4: DFPH-a.01_10R59P_LC Fab light chain

MacromoleculeName: DFPH-a.01_10R59P_LC Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 23.266779 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSR LSASVGDRVT VTCRASQDID KDLSWFQQKP GKAPTLLIFT ASSLQTGVPS RFSGSGSGTE FTLTISSLQP EDFATYFCQ QDYSFPLTFG GGTKVDLKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSR LSASVGDRVT VTCRASQDID KDLSWFQQKP GKAPTLLIFT ASSLQTGVPS RFSGSGSGTE FTLTISSLQP EDFATYFCQ QDYSFPLTFG GGTKVDLKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 18 / 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

Concentration5.8 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / 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) / Number grids imaged: 1 / Number real images: 9013 / Average electron dose: 43.5 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: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3545061
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8euv

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 347691
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationNumber classes: 54 / Software - Name: cryoSPARC (ver. 3.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9q0w:
Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab

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