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- EMDB-51554: LN02-ML85 Fab in complex with crosslinked DS-SOSIP HIV-1 Env trimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51554
TitleLN02-ML85 Fab in complex with crosslinked DS-SOSIP HIV-1 Env trimer
Map data
Sample
  • Complex: Complex of HIV-1 DS-SOSIP Env trimer with LN02-ML85 Fab
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Heavy chain Fab of antibody LN02-ML85
    • Protein or peptide: Light chain of antibody LN02-ML85
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / complex / antibody / Fab / Env / VIRAL PROTEIN
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPedenko B / Effantin G / Weissenhorn W
Funding support France, 1 items
OrganizationGrant numberCountry
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)C7H-LXG19M66-PEDENKO France
CitationJournal: To Be Published
Title: Structure of LN02-ML85 Fab in complex with DS-SOSIP
Authors: Pedenko B / Effantin G / Weissenhorn W / Fenwick C
History
DepositionSep 16, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51554.png

Downloads & links

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Map

FileDownload / File: emd_51554.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 352 pix.
= 295.68 Å		0.84 Å/pix.
x 352 pix.
= 295.68 Å		0.84 Å/pix.
x 352 pix.
= 295.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0456
Minimum - Maximum-0.16667001 - 0.46723628
Average (Standard dev.)0.001499982 (±0.0174434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 295.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51554_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_51554_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 : Complex of HIV-1 DS-SOSIP Env trimer with LN02-ML85 Fab

EntireName: Complex of HIV-1 DS-SOSIP Env trimer with LN02-ML85 Fab
Components
  • Complex: Complex of HIV-1 DS-SOSIP Env trimer with LN02-ML85 Fab
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Heavy chain Fab of antibody LN02-ML85
    • Protein or peptide: Light chain of antibody LN02-ML85
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of HIV-1 DS-SOSIP Env trimer with LN02-ML85 Fab

SupramoleculeName: Complex of HIV-1 DS-SOSIP Env trimer with LN02-ML85 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / 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: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.143459 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDDYKDDD D K

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: Heavy chain Fab of antibody LN02-ML85

MacromoleculeName: Heavy chain Fab of antibody LN02-ML85 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.790012 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAPLPESGPG VVRPTGTLSL TCTAAYGSIS RHFWGWVRQS PQGTLEWIAH MHHLGVKYVN PSLKNRVSIS MDTSKNQMSL TLKTVTATD AAKYHCVRMG ARMSDIAFFS FGDWGPGSLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QAPLPESGPG VVRPTGTLSL TCTAAYGSIS RHFWGWVRQS PQGTLEWIAH MHHLGVKYVN PSLKNRVSIS MDTSKNQMSL TLKTVTATD AAKYHCVRMG ARMSDIAFFS FGDWGPGSLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPK

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Macromolecule #4: Light chain of antibody LN02-ML85

MacromoleculeName: Light chain of antibody LN02-ML85 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.975432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYVLGQSSSM SVAPGQTAKI SCWGYYMGTK PVNWYQLKPG RAPSLIISYD DERASGTPAR FSGSHSGSTA TLTISNVVPA DEADYFCQV WDSYYEEIYF GGGTALTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
SYVLGQSSSM SVAPGQTAKI SCWGYYMGTK PVNWYQLKPG RAPSLIISYD DERASGTPAR FSGSHSGSTA TLTISNVVPA DEADYFCQV WDSYYEEIYF GGGTALTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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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: 29 / 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98398
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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