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- EMDB-41461: Cryo-EM structure of BG505 Env mutant A517E in complex with antib... -

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Basic information

Entry
Database: EMDB / ID: EMD-41461
TitleCryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
Map data
Sample
  • Complex: HIV-1 Env trimer complexed with antibody Fab
    • Complex: antibody Fab
      • Protein or peptide: antibody ACS202 Fab heavy chain
      • Protein or peptide: antibody ACS202 Fab light chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordscomplex / viral antigen / antibody / VIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN / IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 ...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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang S / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2024
Title: Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide.
Authors: Mateo Reveiz / Kai Xu / Myungjin Lee / Shuishu Wang / Adam S Olia / Darcy R Harris / Kevin Liu / Tracy Liu / Andrew J Schaub / Tyler Stephens / Yiran Wang / Baoshan Zhang / Rick Huang / ...Authors: Mateo Reveiz / Kai Xu / Myungjin Lee / Shuishu Wang / Adam S Olia / Darcy R Harris / Kevin Liu / Tracy Liu / Andrew J Schaub / Tyler Stephens / Yiran Wang / Baoshan Zhang / Rick Huang / Yaroslav Tsybovsky / Peter D Kwong / Reda Rawi /
Abstract: Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To ...Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1 fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with substitutions to negatively charged amino acids at residue positions 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV-1; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structural analysis of the naturally elicited ACS202 antibody in complex with the HIV-1 Env trimer with an alanine 517 to glutamine substitution suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence, perhaps reflecting the immunization with fusion peptide of the vaccine-elicited antibodies.
History
DepositionAug 4, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41461.png

Downloads & links

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Map

FileDownload / File: emd_41461.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 371.84 Å		0.83 Å/pix.
x 448 pix.
= 371.84 Å		0.83 Å/pix.
x 448 pix.
= 371.84 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: 0.0435
Minimum - Maximum-0.21134672 - 0.6992145
Average (Standard dev.)0.0006788692 (±0.014313555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 371.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41461_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41461_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Env trimer complexed with antibody Fab

EntireName: HIV-1 Env trimer complexed with antibody Fab
Components
  • Complex: HIV-1 Env trimer complexed with antibody Fab
    • Complex: antibody Fab
      • Protein or peptide: antibody ACS202 Fab heavy chain
      • Protein or peptide: antibody ACS202 Fab light chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: HIV-1 Env trimer complexed with antibody Fab

SupramoleculeName: HIV-1 Env trimer complexed with antibody Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: gp41 and gp120 expressed as a single polypeptide, post translationally cleaved; antibody expressed and purified separately; purified Env trimer and Fab were mixed to make complex
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505

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Supramolecule #2: antibody Fab

SupramoleculeName: antibody Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505
Molecular weightTheoretical: 17.134404 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGEVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHLLKLGVW GFKQLQARVL AVERYLEVQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEIGNYTQ IIYGLLEESQ FQQEINEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505
Molecular weightTheoretical: 53.262453 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 SACTQICPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CKNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNIIVQ FNTPVQINCT RPNNMTRKSI RIGPGQAFYA LGDIIGDIRQ PHCTVSKATW NETLGKVVKQ LRK HFGNNT IIFFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RVGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: antibody ACS202 Fab heavy chain

MacromoleculeName: antibody ACS202 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.295486 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGGSLRL SCAASGFAFK DFGMHWVRQA PGKGLEWVAV IGGGHGQHQS YSESVKGRFA ITRDNEKNKL YLHMDRLRT EDTAVYYCAK DRLGRPWNIG GRLVYYYYGM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVQLVESGGG VVQPGGSLRL SCAASGFAFK DFGMHWVRQA PGKGLEWVAV IGGGHGQHQS YSESVKGRFA ITRDNEKNKL YLHMDRLRT EDTAVYYCAK DRLGRPWNIG GRLVYYYYGM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCD

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Macromolecule #4: antibody ACS202 Fab light chain

MacromoleculeName: antibody ACS202 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.470197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIRMTQSPSS LSASVGDRVT ITCQASQDIK KSLNWYRQKP GKAPELLIHD ASILQTGVPS AFTASGSGTH FSFVINKLQP EDVGTYFCQ EYENLQFTFG PGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
AIRMTQSPSS LSASVGDRVT ITCQASQDIK KSLNWYRQKP GKAPELLIHD ASILQTGVPS AFTASGSGTH FSFVINKLQP EDVGTYFCQ EYENLQFTFG PGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 369 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 mg/mL
BufferpH: 7.4 / Details: PBS with 0.1 mM DTT
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vi0

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 635332
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: UCSF Chimera (ver. 1.16)
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8tox:
Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

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