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- EMDB-19665: Fab4251-DS-SOSIP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19665
TitleFab4251-DS-SOSIP complex
Map data
Sample
  • Complex: Envelope glycoprotein Human immunodeficiency virus 1 with Fab
    • Protein or peptide: variable heavy chain
    • Protein or peptide: variable light chain
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / VIRAL PROTEIN
Biological speciesHIV whole-genome vector AA1305#18 (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsNortier P / Perez L
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Res Sq / Year: 2024
Title: RAIN: a Machine Learning-based identification for HIV-1 bNAbs.
Authors: Laurent Perez / Mathilde Foglierini /
Abstract: Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune ...Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoire is still lacking. Here, we developed a straightforward computational method for apid utomatic dentification of bAbs ) based on Machine Learning methods. In contrast to other approaches using one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of novel HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
History
DepositionFeb 17, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19665.png

Downloads & links

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Map

FileDownload / File: emd_19665.map.gz / Format: CCP4 / Size: 198.4 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 382 pix.
= 279.918 Å		0.73 Å/pix.
x 374 pix.
= 274.056 Å		0.73 Å/pix.
x 364 pix.
= 266.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.73277 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.17637661 - 0.63862175
Average (Standard dev.)0.0035650155 (±0.016746514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-12-7-13
Dimensions374364382
Spacing364374382
CellA: 266.7283 Å / B: 274.056 Å / C: 279.91815 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19665_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19665_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Envelope glycoprotein Human immunodeficiency virus 1 with Fab

EntireName: Envelope glycoprotein Human immunodeficiency virus 1 with Fab
Components
  • Complex: Envelope glycoprotein Human immunodeficiency virus 1 with Fab
    • Protein or peptide: variable heavy chain
    • Protein or peptide: variable light chain
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Envelope glycoprotein Human immunodeficiency virus 1 with Fab

SupramoleculeName: Envelope glycoprotein Human immunodeficiency virus 1 with Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
Molecular weightTheoretical: 400 kDa/nm

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Macromolecule #1: variable heavy chain

MacromoleculeName: variable heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.951986 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHVMQSGDQ VKKPGASVQV SCTTSGSSFI EDSLHWIQQV PGQEPEWLGW VNPRHGAVNY SWKIRDRITM TRDISKSTMY VQMRGLQSD DTAMYYCAKS RRGANWALYW GWGTRITVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
QVHVMQSGDQ VKKPGASVQV SCTTSGSSFI EDSLHWIQQV PGQEPEWLGW VNPRHGAVNY SWKIRDRITM TRDISKSTMY VQMRGLQSD DTAMYYCAKS RRGANWALYW GWGTRITVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PK

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Macromolecule #2: variable light chain

MacromoleculeName: variable light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.257809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPSY LAASVGDRVT ITCRESNDLN WYLQRPGKPP KLLISGASKL ERGVPSRFRG SSSGSLTISG LQPEDIGTYY CQVFEFFGG GTRVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD S TYSLSSTL ...String:
DIQLTQSPSY LAASVGDRVT ITCRESNDLN WYLQRPGKPP KLLISGASKL ERGVPSRFRG SSSGSLTISG LQPEDIGTYY CQVFEFFGG GTRVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD S TYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #3: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3
Details: Envelope glycoprotein gp120|Human immunodeficiency virus 1
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
Molecular weightTheoretical: 49.558484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDHNV WATHACVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL RDKKQKVYSL FYRLDVVQIK EYRLINCNTS ACTQACPKVS F EPIPIHYC ...String:
AENLWVTVYY GVPVWKDAET TLFCASDHNV WATHACVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL RDKKQKVYSL FYRLDVVQIK EYRLINCNTS ACTQACPKVS F EPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EVMIRSENIT NNAKNILVQF NT PVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRKHFGNNTI IRFANSSGGD LEV TTHSFN CGGEFFYCNT SGLFNSTWIS NSNDSITLPC RIKQIINMWQ RIGQCMYAPP IQGVIRCVSN ITGLILTRDG GSTN STTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKR

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Macromolecule #4: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
Molecular weightTheoretical: 14.561529 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSTVWGI KQLQARVLAV ERYLRDQQLL GIWGCSGKLI CCTNVPWNSS WSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA L

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 17 / 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 mg/mL
BufferpH: 6
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 4 / Number real images: 15163 / Average electron dose: 39.89 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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:

4tvp

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72497
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8s2e:
Fab4251-DS-SOSIP complex

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