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- EMDB-50092: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-50092
TitleHIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with three copies of ELC07 broadly neutralizing antibody.
Map dataLocally filtered map with deepEMhancer
Sample
  • Complex: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
    • Complex: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer
      • Protein or peptide: Transmembrane protein gp41
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: ELC07 broadly neutralizing antibody
      • Protein or peptide: ELC07 heavy chain
      • Protein or peptide: ELC07 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / envelope glycoprotein / gp140 / neutralizing antibody / VIRAL PROTEIN
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 / 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: 3.02 Å
AuthorsHope J / Alguel Y / Nans A / Cherepanov P
Funding support United States, United Kingdom, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
The Francis Crick InstituteCC2058 United Kingdom
Wellcome TrustCC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Cancer Research UKCC2058 United Kingdom
CitationJournal: To Be Published
Title: TITLE: Preservation of memory B cell homeostasis in an individual producing broadly neutralizing antibodies against HIV-1
Authors: Griffith S / Muir L / Suchanek O / Hope J / Pade C / Gibbons G / Tuong K / Fung A / Touizer E / Rees-Spear C / Nans A / Roustan C / Alguel Y / Fink D / Orkin C / Deayton J / Anderson J / ...Authors: Griffith S / Muir L / Suchanek O / Hope J / Pade C / Gibbons G / Tuong K / Fung A / Touizer E / Rees-Spear C / Nans A / Roustan C / Alguel Y / Fink D / Orkin C / Deayton J / Anderson J / Gupta RK / Doores KJ / Cherepanov P / McKnight A / Clatworthy M / McCoy LE
History
DepositionApr 15, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50092.png

Downloads & links

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Map

FileDownload / File: emd_50092.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered map with deepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.02846783 - 1.6101978
Average (Standard dev.)0.0012479275 (±0.022757655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50092_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally filtered map generated in cryoSPARC

Fileemd_50092_additional_1.map
AnnotationLocally filtered map generated in cryoSPARC
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_50092_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_50092_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_50092_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com...

EntireName: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
Components
  • Complex: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
    • Complex: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer
      • Protein or peptide: Transmembrane protein gp41
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: ELC07 broadly neutralizing antibody
      • Protein or peptide: ELC07 heavy chain
      • Protein or peptide: ELC07 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com...

SupramoleculeName: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer

SupramoleculeName: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: ELC07 broadly neutralizing antibody

SupramoleculeName: ELC07 broadly neutralizing antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 19.10359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGSGLND I FEAQKIEW HE

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 / Strain: BG505 SOSIP.664
Molecular weightTheoretical: 57.945977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: ELC07 heavy chain

MacromoleculeName: ELC07 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.586055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG EVQLVQSGAE LKKAGSSVKL SCQAYGVAFS TYSFHWVRQA PGQGLEWLGG FIPLVGKPNY TNKFRGRLT ITADESARTT YMELRSLRSD DTAIYYCAGG GAYSSGGGRF HYFGMAVWGQ GSTVTVSSAS TKGPSVFPLA P SSKSTSGG ...String:
METDTLLLWV LLLWVPGSTG EVQLVQSGAE LKKAGSSVKL SCQAYGVAFS TYSFHWVRQA PGQGLEWLGG FIPLVGKPNY TNKFRGRLT ITADESARTT YMELRSLRSD DTAIYYCAGG GAYSSGGGRF HYFGMAVWGQ GSTVTVSSAS TKGPSVFPLA P SSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TK VDKRVEP KSCGSGENLY FQSAGHHHHH H

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Macromolecule #4: ELC07 light chain

MacromoleculeName: ELC07 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.599775 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTQTPASLLF LLLLWLPGAK CDIQLTQSPS TLSAPVGAGV TITCQASQSI SNGLAWYQQK PGRAPKMLIT EGSSLKSGVP DRFRGSGSG THFILTISDL QPDDSATYFC QQYNTFPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
MTQTPASLLF LLLLWLPGAK CDIQLTQSPS TLSAPVGAGV TITCQASQSI SNGLAWYQQK PGRAPKMLIT EGSSLKSGVP DRFRGSGSG THFILTISDL QPDDSATYFC QQYNTFPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 24 / 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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTristris

Details: 150 mM NaCl, 50 mM Tris-HCl, pH 7.5
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / 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) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35337
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8fr6

chain_id: A, source_name: PDB, initial_model_type: experimental model

8fr6

chain_id: C, source_name: PDB, initial_model_type: experimental model
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
chain_id: L, source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9f02:
HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with three copies of ELC07 broadly neutralizing antibody.

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